Thanks for the reply but it seems I messed up my 3DS big time in a way that makes no sense at all o.o I'll report back in a moment!
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Okay I'll write what I did and my system specs:
EU new 3DS running 11.0E with A9LH v2 and Luma3DS 6 stable with a 64gb SanDisk microSD.
I made a backup with Hourglass9 and a CTRNAND backup with Decrypt9 before doing anything. I loaded up FBI 2.x (can't check the exact version at the moment) and searched for the TitleID which I couldn't find. In frustration I simply deleted the title "HomeMenu" and tried to install the clean .cia again which didn't work and it still said "Title Already Exists!" so I obviously deleted the wrong title. Rebooting my 3DS it was unsurprisingly bricked and rebooted to a black screen after BootAnim9. No problem I booted up Hourglass9 which verified the backup fine and restore it, the 3DS rebooted normally and was working 100% fine so I shut it off. Now when I wanted to turn it on again to check what FBI version I have it booted again to a black-screen after BootAnim9, multiple times o.o
Right now I'm restoring the backup again, what is going on with my 3DS?
EDIT: Phew okay after the second restore it boots normally consecutively again, so back to the original problem
How do I delete the title in FBI? I'm using version 2.3.3