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I am not clear on what you mean with "deleted". Are we talking about the archive files stored on disk, or the backup records stored in the database?

Akeeba Backup will remove backup archive files (but not backup archive records) when the quota settings kick in.

Akeeba Backup will remove backup records which do not have valid archive record (obsolete records) based on the Obsolete Records Quotas setting.

In no other case will Akeeba Backup remove backup archive files or records.

If you have set up your backup profile to use the same name for every backup (there are no per-backup naming components, such as [DATE]) then Akeeba Backup will of course overwrite your previous backup with the new backup archive file. This, however, is a problem if used together with quota settings as it may end up deleting the (only) backup archive set on your site. Together with obsolete record quotas it will also end up deleting backup records which previously appeared as OK (since all of them were pointing to the one and only backup archive which was present on your disk, but now got deleted by the quota settings, therefore they immediately became obsolete).

All right. Let's forget the fact that it's always the same code running regardless of how you take a backup. Let's forget the fact that quota settings only run at the end of the backup based on the records kept in the database, the configuration of the backup profile you are backing up with, and only operate on backup archives created by the same backup profile. Let's also forget the fact that the quota code has not changed at all since August 30th, 2022 — over a year ago — and nobody has reported anything similar, which would be unheard of if there's a bug of the magnitude you allege given the fact that we have thousands of clients using the software on hundreds of thousands of servers and we never had a major issue which went unreported by anyone for longer than 3 hours after making a release that included said bug (this is a fact, unfortunately, and it definitely keeps us on our toes, but that's another story for another time).

Let's follow the scientific method. We will make a hypothesis and test it.

We shall hypothesize there is an as yet unidentified bug. For this assumption to hold, the bug will be reproducible following your instructions.

So, I start by creating a brand new Joomla! 4.3.4 site on PHP 8.1.24 and install Akeeba Backup Professional 9.8.1 on it. To keep it fair, I downloaded both Joomla! and Akeeba Backup Professional from their respective official download sites instead of using my local copies.

I am going through Akeeba Backup's Configuration Wizard.

At this point, there are quotas set up: count quotas, set to 3. I am taking 7 backups from the backend of the site.

As expected, the latest 3 backups (IDs 7, 6, and 5) are OK and the other 4 (IDs 4, 3, 2, and 1) show as Obsolete. This proves that the quota settings were respected. But that is not what you want me to test.

So, as per your reproduction instructions, I am completely turning off all quota settings.I do keep the "Obsolete records to keep" to its default value, 50. I am not making any other changes to the configuration.

I am taking another 6 backups.

As expected, I see that records from 13 down to 5 are shown as OK and the original four (1, 2, 3, and 4) are still shown as Obsolete. This proves that disabling quotas had the intended effect in the backend.

Now, let's take the CLI backup.

php /var/www/client/cli/joomla.php akeeba:backup:take --description="Automated Backup on [YEAR]-[MONTH]-[DAY] - [TIME]"

And yes, before you ask, I did run it with a CRON job set to run a minute after I edited my crontab with crontab -e:

29 22 * * * php /var/www/client/cli/joomla.php akeeba:backup:take --description="Automated Backup on [YEAR]-[MONTH]-[DAY] - [TIME]"

As expected, I see that records from 14 down to 4 are shown OK and the original four are obsolete:

$ php /var/www/client/cli/joomla.php akeeba:backup:list

List of Akeeba Backup records matching your criteria
====================================================

 ---- --------------------------------------------------- --------- --------------------- --------------------- ---------- --------- ------ ------------ --------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------- ----------- --------- --------------------------- ------------ ----------------- ------------ -------- -------- ---------- ---------------- ---------- 
  id   description                                         comment   backupstart           backupend             status     origin    type   profile_id   archivename                                                     absolute_path                                                                                                                    multipart   tag       backupid                    filesexist   remote_filename   total_size   frozen   instep   meta       hasRemoteFiles   size      
 ---- --------------------------------------------------- --------- --------------------- --------------------- ---------- --------- ------ ------------ --------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------- ----------- --------- --------------------------- ------------ ----------------- ------------ -------- -------- ---------- ---------------- ---------- 
  14   Automated Backup on 2023-10-23 - 192920                       2023-10-23 19:29:00   2023-10-23 19:29:04   complete   cli       full   1            site-client.local.web-20231023-192900utc-TK69tt1_wWB6hcET.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192900utc-TK69tt1_wWB6hcET.jpa   1           cli       id-20231023-192920-810041   1                              34114864     0        1        ok                          34114864  
  13   Backup taken on Monday, 23 October 2023 19:26 UTC             2023-10-23 19:26:15   2023-10-23 19:26:19   complete   backend   full   1            site-client.local.web-20231023-192615utc-Jov6sIYiJ3dtDoBP.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192615utc-Jov6sIYiJ3dtDoBP.jpa   1           backend   id-20231023-192615-629368   1                              34114779     0        1        ok                          34114779  
  12   Backup taken on Monday, 23 October 2023 19:26 UTC             2023-10-23 19:26:10   2023-10-23 19:26:14   complete   backend   full   1            site-client.local.web-20231023-192610utc-EzrYsRa2vaRwXpmS.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192610utc-EzrYsRa2vaRwXpmS.jpa   1           backend   id-20231023-192610-642392   1                              34114727     0        1        ok                          34114727  
  11   Backup taken on Monday, 23 October 2023 19:26 UTC             2023-10-23 19:26:05   2023-10-23 19:26:09   complete   backend   full   1            site-client.local.web-20231023-192605utc-BpaMmPIy8PGCZDas.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192605utc-BpaMmPIy8PGCZDas.jpa   1           backend   id-20231023-192605-708449   1                              34114667     0        1        ok                          34114667  
  10   Backup taken on Monday, 23 October 2023 19:25 UTC             2023-10-23 19:25:58   2023-10-23 19:26:04   complete   backend   full   1            site-client.local.web-20231023-192558utc-CnYIwJgUc0udxnDM.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192558utc-CnYIwJgUc0udxnDM.jpa   1           backend   id-20231023-192558-321869   1                              34114607     0        1        ok                          34114607  
  9    Backup taken on Monday, 23 October 2023 19:25 UTC             2023-10-23 19:25:53   2023-10-23 19:25:57   complete   backend   full   1            site-client.local.web-20231023-192553utc-WGTLcdR2ki0CBWWJ.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192553utc-WGTLcdR2ki0CBWWJ.jpa   1           backend   id-20231023-192553-75651    1                              34114556     0        1        ok                          34114556  
  8    Backup taken on Monday, 23 October 2023 19:25 UTC             2023-10-23 19:25:42   2023-10-23 19:25:46   complete   backend   full   1            site-client.local.web-20231023-192542utc-un_gwSXR2HZKzmdq.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192542utc-un_gwSXR2HZKzmdq.jpa   1           backend   id-20231023-192542-107403   1                              34114501     0        1        ok                          34114501  
  7    Backup taken on Monday, 23 October 2023 19:23 UTC             2023-10-23 19:23:11   2023-10-23 19:23:15   complete   backend   full   1            site-client.local.web-20231023-192311utc-ZeG4TixHxYga55w_.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192311utc-ZeG4TixHxYga55w_.jpa   1           backend   id-20231023-192311-391422   1                              34114425     0        1        ok                          34114425  
  6    Backup taken on Monday, 23 October 2023 19:23 UTC             2023-10-23 19:23:06   2023-10-23 19:23:10   complete   backend   full   1            site-client.local.web-20231023-192306utc-YJZ0BOQI1S8Qklwc.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192306utc-YJZ0BOQI1S8Qklwc.jpa   1           backend   id-20231023-192306-235857   1                              34114372     0        1        ok                          34114372  
  5    Backup taken on Monday, 23 October 2023 19:23 UTC             2023-10-23 19:23:00   2023-10-23 19:23:05   complete   backend   full   1            site-client.local.web-20231023-192300utc-L7hAqrplLxcqstzY.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192300utc-L7hAqrplLxcqstzY.jpa   1           backend   id-20231023-192300-806141   1                              34114322     0        1        ok                          34114322  
  4    Backup taken on Monday, 23 October 2023 19:22 UTC             2023-10-23 19:22:55   2023-10-23 19:22:59   complete   backend   full   1            site-client.local.web-20231023-192255utc-9oKWreecA0Etlh2_.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192255utc-9oKWreecA0Etlh2_.jpa   1           backend   id-20231023-192255-674521   0                              34114257     0        1        obsolete                              
  3    Backup taken on Monday, 23 October 2023 19:22 UTC             2023-10-23 19:22:50   2023-10-23 19:22:54   complete   backend   full   1            site-client.local.web-20231023-192250utc-fiqTLHbG-G-zyZMN.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192250utc-fiqTLHbG-G-zyZMN.jpa   1           backend   id-20231023-192250-475081   0                              34114209     0        1        obsolete                              
  2    Backup taken on Monday, 23 October 2023 19:22 UTC             2023-10-23 19:22:45   2023-10-23 19:22:49   complete   backend   full   1            site-client.local.web-20231023-192245utc-Y7nP5z6KNvGrdaHA.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192245utc-Y7nP5z6KNvGrdaHA.jpa   1           backend   id-20231023-192245-139249   0                              34114155     0        1        obsolete                              
  1    Backup taken on Monday, 23 October 2023 19:22 UTC             2023-10-23 19:22:22   2023-10-23 19:22:30   complete   backend   full   1            site-client.local.web-20231023-192222utc-ZXZTIi26vJbbOlBA.jpa   /var/www/client/administrator/components/com_akeebabackup/backup/site-client.local.web-20231023-192222utc-ZXZTIi26vJbbOlBA.jpa   1           backend   id-20231023-192222-377503   0                              34114069     0        1        obsolete                              
 ---- --------------------------------------------------- --------- --------------------- --------------------- ---------- --------- ------ ------------ --------------------------------------------------------------- -------------------------------------------------------------------------------------------------------------------------------- ----------- --------- --------------------------- ------------ ----------------- ------------ -------- -------- ---------- ---------------- ---------- 

$ls /var/www/client/administrator/components/com_akeebabackup/backup
akeeba.backend.id-20231023-192300-806141.log.php
akeeba.backend.id-20231023-192306-235857.log.php
akeeba.backend.id-20231023-192311-391422.log.php
akeeba.backend.id-20231023-192542-107403.log.php
akeeba.backend.id-20231023-192553-75651.log.php
akeeba.backend.id-20231023-192558-321869.log.php
akeeba.backend.id-20231023-192605-708449.log.php
akeeba.backend.id-20231023-192610-642392.log.php
akeeba.backend.id-20231023-192615-629368.log.php
akeeba.cli.id-20231023-192900-810041.log.php
akeeba.log.php
index.htm
index.html
index.php
site-client.local.web-20231023-192300utc-L7hAqrplLxcqstzY.jpa
site-client.local.web-20231023-192306utc-YJZ0BOQI1S8Qklwc.jpa
site-client.local.web-20231023-192311utc-ZeG4TixHxYga55w_.jpa
site-client.local.web-20231023-192542utc-un_gwSXR2HZKzmdq.jpa
site-client.local.web-20231023-192553utc-WGTLcdR2ki0CBWWJ.jpa
site-client.local.web-20231023-192558utc-CnYIwJgUc0udxnDM.jpa
site-client.local.web-20231023-192605utc-BpaMmPIy8PGCZDas.jpa
site-client.local.web-20231023-192610utc-EzrYsRa2vaRwXpmS.jpa
site-client.local.web-20231023-192615utc-Jov6sIYiJ3dtDoBP.jpa
site-client.local.web-20231023-192900utc-TK69tt1_wWB6hcET.jpa
web.config

Since taking a backup from the CLI with all quota settings disabled did not result in any backup archives being deleted we conclude, as the result of using the scientific method, that the hypothesised bug does not exist.

I consider it far more likely that the host deleted the backup archives. They are big files and they look “suspicious” because they have a non-standard extension, they are big, they have compressed data, and it would not be the first time we see a host deleting files without asking because they mistook them for something sinister. I strongly recommend that you store your backup archives off-site to avoid issues like that in the future.

Also note that I am replying to this ticket assuming that you know what you are talking about. I am not making this statement to insult you. I just know that most of the times someone comes here to ask help for a “bug” in quota management we invariably see that they misunderstood how quotas work. It's very important to understand that the quota settings are per profile, apply only to the backups taken with that profile, and that they are calculated based on the information in the database (the database records you see in the Manage Backups page). If you only edited the quota settings in profile #1, these changes will not apply to profile #2 (the one you are using).

Moreover, I am not even considering far more mundane issues all of us have inflicted upon ourselves at one time or another, such as using the same folder as the backup output and Joomla! temporary directory, accidentally deleting all files in the wrong folder, or creating an automation which does what we told it to do and not what we intended it to do.

Yeah, it really is weird. I was thinking about this this morning.

Are you sure nobody else has access to your site over FTP / SFTP? I would definitely prefer going the paranoid route and change all passwords. I recommend using a password manager to generate 64 character passwords consisting of lowercase and uppercase letters, numbers, and punctuation (basically, everything you can type on your keyboard).

I would also start dumping the list of files of the backup folder to a file at the end of the backup, e.g. changing the CRON command line to

/usr/local/bin/php /[my-site-path]/cli/joomla.php akeeba:backup:take --profile=2 --description="Automated Backup on [YEAR]-[MONTH]-[DAY] - [TIME]"; ls /wherever/your/backup/folder/is > /[my-site-path]/../list-of-backups.txt

You get the idea. If you see backups disappearing again you can look at the list of files. If the files were not missing from the list, they were not removed by Akeeba Backup. So, that gives you some ammo to go to your host and say hey, why are you guys removing my backups.

The exit code is really a standard thing. Please read an introduction for their use in Linux and the Bash shell at https://www.baeldung.com/linux/status-codes