Ok so your games are on internal right, Are you sure Openmanager is set up to use the same folder as your previous manager was,I suspect this is the issue?
You can try pressing L2+start while in open manager to select different a game folder.
If that doesnt work what I recommend doing to test this is try moving one game (use a small one!) into one of the other possible Open manager folders and then check if Open manager sees the game,If you cant see the game in openmanager try another folder (eg, If all your games are in Dev_hdd00\Game\LAUN12345\ try move one to the OMAN12345 folder, or vice versa) If there is any other open manager folders in your Dev_hdd00\Game\ try them too! (Normally they will be named ''OMANxxxxx'' or ''LAUNxxxxx'')
If none of that works you will need to backup your backups off the internal HDD using either Comgenies file manager
or FTP server
and start again...