I've been tidying up all of my systems for the past few days. on the vita, I've uninstalled all unnecessary apps. of the remaining apps, I noticed that some of the apps were missing backgrounds. I had deleted all of appmeta to replace with a backup I had made, so some files may have gotten corrupted or not transferred. some folders in there seem to be protected via ftp, so I erased the rest through vita shell. speaking of which, I found a possible bug with vita shell's usb connection. the pspemu folder shows up as blank, so you can't use psp content manager to sort content.
anyway, the system gets the background image from ur0:appmeta/title id/livearea/contents folder. it's recorded in the appinfo table of the app.db in ur0:shell/db. I backed that up too just in case I needed to rebuild the database. I was forced to rebuild the database. when I got back to the livearea, all apps, but molecular shell and vita shell were gone. I kept a copy of those apps on internal memory just in case I needed them. what I found is that the config.txt is recreated, but if you replace the one in ur0, it won't fix it. the config.txt is actually recreated on ux0 too, which overrides the one on ur0, so you have to delete it. I think there's another config.txt in vs0 which would probably get removed if you reinstalled the firmware. I saw a thread somewhere regarding this issue. I think the person restored the system or formatted the memory card instead of just deleting the config.txt on ux0 to fix the problem.