Support

That's a blast from the past! I think I haven't had a ticket about that in 4 or 5 years :)

You cannot restore a Joomla! 3 site on top of a Joomla! 2.5 site or vice versa. The way Joomla locates its files and the fact that restoring a site does not remove existing files mean that you get a broken site.

First, take a local copy of all your backup archives. Double check and triple check they are there and that they can be extracted (e.g. with Akeeba eXtract Wizard).

Next up, big leap of faith, delete your site's files. At the very least delete the administrator, cli, components, includes, language, layouts, libraries, media, modules, plugins and templates folders and all their contents including their subdirectories.

Then extract the backup archive using Kickstart and restore your site to its last working state from a backup archive which you upload to your site.

For what it's worth, before you upgrading Joomla! you should disable all extensions on your site. After upgrading to Joomla! 3 you will need to perform several upgrades to get to Joomla! 3.9.3. Then start updating all of the extensions on your site with Joomla! 3.9 compatible versions. If something is not available you may have to replace it.

It's best if you do this work on a local server. When you're done follow the steps I outlined above to remove your old Joomla! 2.5 site and restore the new Joomla! 3.9 site. Your downtime should be minimal, typically less than 10' (it largely depends on how fast your server can delete files and folders).

When you tried to upgrade it the site became (at least partially) Joomla! 3. That is, some J3 files were written to disk. Then you tried to restore a Joomla! 2.5 on top of it.

As I said, when you extract a backup archive only new files are written. Existing files are not deleted. The problem is that J3 moved or renamed some files. These files do not exist in J2.5. However, the way the Joomla! automatic core file loading works the J3 file locations have precedence to the locations of the J2.5 files. So what happens is that you end up running a frankensite which tries to load code from both J2.5 and J3. This mix is what kills the site.

I have seen that plenty of times when people were upgrading their sites from 2.5 to 3.x. What I wrote before is accurate.

Regarding the database, at this point I would recommend removing all tables as well. This is NOT going to affect going back to Joomla! 2.5 but will affect your ability to go from Joomla! 2.5 to Joomla! 3. You see, the Joomla! updates are written on the assumption that you are going from 2.5 to 3, i.e. the new tables introduced in Joomla! 3 are not already present. If they are weird things happen, including the possibility of a partial upgrade. Therefore nuking the database (removing all tables) is a good idea ;)