Jemuel, you had a duplicate thread. I deleted it.
People were having problems with FPSE overwriting save files sometimes when upgrading, and losing savefiles when trundling, so...
Schtruck moved the save files to /sdcard/.fpse. Now, the backup option backs up configuration info, but not the save game info, because the save game info isn't in the install folder.
Of you didn't overwrite your sdcard when you reloaded your phone, they'll be in /sdcard/.fpse. You need to be using a file browser that can see hidden files/folders to see it.