Sorry for delay. It is in any case only testing server. I was busy.
Nope, it didn't solved anything (but I was supprised). I can't understand what is going on here. Site was fine (settings), but SSL expired (no idea why cron not working). Then after I manually created renewal, I'm dropped on LAMP page. Now I can see how actually your script change previously set files (configuration).
Any idea how to regain access to Wordpress (without SSL is also ok, with prefix is also ok)?