How many games are we talking here?Didn't want to make a new thread and this seems as good a Vita OT as any, so:
Booted up my Vita in the first time in a while, and it gave me an error about the memory card being ejected, so I reset it.
Seems like all my digital games are missing, so turn it off, take the card out, back in, turn on.
Then one of my folders is there (have like 2 PS1 folders, 1 PSP, then 2 digital Vita), check Content Manager and all the games are there, the other folders just aren't showing up so I can't actually access them.
Turned off again, boot into safe mode or whatever and go rebuild database. All that did was take the games I could get to before out of their folder (so everything is just on the base menu). Everything else is still MIA.
Guess I'll just delete everything via Content Manager and redownload it all? :\
There's a bubble limit, so what might have happened is that when it turfed all your games out of their folders you then ended up with too many to display. You might find that if you start putting things back in bubbles and then restart your vita the "missing" ones will reappear.