remove the sd2vita, then plug it back in. rebuilding the database (app.db) scans your games and uses position/page to reflect their location on the screen. though, I've never been on 3.70, so things may be a little different. however, the problem your having is most likely due to the app.db. for some reason, it's not picking up pirated games. I know it does that on the ps4, which is why it's important to backup the app.db for both systems.
oh, I just thought of something. the tai config.txt has probably been recreated. create the one you want on the sd2vita micro sd. it will override what's in ur0 (your plugins are still there, but a new, empty config.txt has been created). anyway, cut and paste the config.txt from ux0 to ur0.
