Sorry about the wait, I was at work.
I've noticed that the system still runs perfectly fine, even with the extra titles installed. Everything can be accessed as normal except for titles that require you to have the latest firmware version. It's not even semi-bricked, it just has lots of unneeded titles on there. The system still thinks it's on 9.2.0-20U, and I'm 99% sure the native_firm is on 9.2.0-20U as well.
Anyways, I can still run the memchunkhax2 version of sysupdater. After installing the 10.3 eur package, I was still able to downgrade the mismatched titles left over from 10.3 that had the same titleids. I just can't use any homebrew that requires arm9 access.
As for hardmodding, I would, but this 3DS is my friend's, and I'm not sure how he'd feel about a hardmod, and if it'd be important enough for him in the first place.
While I understand that messing with system titles is dangerous, what could possibly happen if I only uninstall the european system titles? Since everything works, that means that it's only using the titles for the correct region, so it should be safe to delete the extra titles. Could I get a link to the memchunkhax2 version of FBI as well? Google isn't really doing anything for me.