Connect up via FTP and "download" your /dev_hdd0/game/BLES80608/USRDIR/options.ini (and options_default.ini) file(s) and check the games locations are set correctly.
i.e. the sections that start...
# Backup games to these folders:
# Main search folders:
# Secondary search folders:
FYI mine are set as follows:
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I think they are the defaults - don't thnk i ever changed mine - maybe you did though?
I put my games in the /dev_hdd0/GAMES/ folder as that's outside of any manager path and should (fingers crossed) prevent uninstall issues!
- Chances are your games were previously in the \USRDIR\ of the application folder (e.g. LAUN12345\USRDIR\Games\.... ) and this is why they were uninstalled ?
But take my word on this with a little pinch of salt - i'm not the expert on MM/backup managers in general - don't use them too much