@Matej
If you have set those to least amount of time and always display, then go to the course you can't backup, with edit mode on, see if there is a Recyclebin link in the course admin menu. Click it. See anything listed? If so, there should be an option there to delete. Click them.
That should move those items to trashdir. In your cPanel file browser, go to trashdir and see if it's populated with anything. If it has anything in it, delete. That will not harm your moodle.
Things could be stuck in adhoc task. So set the path to php-cli in paths ... the path is the same you see in setting up the cron job. Once you get that set up, go to the scheduled task list ... look for 'clean up' task. Should be a link for 'run now'. If you have a back log of files to be deleted, it will consume a lot of memory and take quite a long time to complete - if that fails, then you might also have to increase PHP variables for time for a script to run as well as max memory to use in Easy Apache setup. You also might have to 'run now' multple times to get things caught up.
Am not an expert in cPanel - don't use it myself - but ... in your cPanel, do you see a Terminal icon? If so, you can run moodle cli commands found in multiple directories of Moodle code. Those take your web service out of the loop and it's just php talking to your database/file system to execute.
All this, as you can tell, has had a 'dominoe' affect.
If you are on a shared hosting plan, you might not have enough access to be able to clean this up from cli and have to suffer via GUI.
'SoS', Ken