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It looks like FEF is being uninstalled even though it should have been marked as a dependency for ATS. Installing ATS without uninstalling it before should work.

Otherwise you can install FEF again on your site, without uninstalling it. Since you're on an old version of ATS you need to install FEF 1. Use the older versions link in our downloads page to find it.

FOF showing it's not being uninstalled is a good thing. It shouldn't because ATS depends on it.

As a fix for the problem you mean?

Correct.

For now, I fixed it by installing the exact same AKeebaBackup that was there before. The ugrade from 3.5 to 4.0 that you published only yesterday is not something happening instantly, I expect stuff to break in the process so I can only do that on staging or a local copy before rolling out.

Very accurate. You definitely need to go through all your template overrides. Things have changed a lot.

I have done very little changes to the frontend CSS. The only major change is the ticket display — the page we are in right now. The structure of the message and user panes has changed, the latter being before the former so we can use CSS Grid to make it responsive, a major problem with mobile display in previous versions.

Moreover, the elements displayed in the user pane have changed a bit, namely the username / flag and the Akeeba Subscriptions integration. 

Since the flag requires Akeeba Subscriptions to display and so does the Akeeba Subscriptions integration but you do not use Akeeba Subscriptions you shouldn't have any problems there.

Everything else is structurally identical. The Blade templates which render each part have changed but the output remains the same. I didn't feel like reinventing the wheel, just polish the pages that most people get to see (tickets display).

I am not entirely sure why this would happen. When we install ATS we mark it as dependent on FEF. This is JSON data stored in the #__akeeba_common table. If for any reason the installation failed to complete, or the table was deleted for some reason then this dependency wouldn't be marked. FEF manifest script's uninstall() would not see a dependency and return true, letting the uninstallation go through.

See the record with key = file_fef. It only has com_akeeba in it. If you change that value to ["com_akeeba", "com_ats"] it will prevent the uninstallation of Akeeba Backup to uninstall FEF.

I have never seen that before. The code used to register the dependency is the one we've been using in all of our software since 2015. I honestly don't know how you'd end up without the dependency recorded.