Has anything changed on the device? Not sure why you would get this, I do not know the cause. Try syncing with your computer/Logbook Pro to make sure your APDL data gets backed up, you may have to remove/reinstall the app.
There's no reason it shouldn't. Did you enter your registration information on the device after reinstalling, if needed? Are you getting any errors? Is Windows seeing the device and refreshing the files on your PC after Logbook Pro syncs it?
It didn't ask to enter any registrarion info, I'm not getting any errors and Windows mobile is seeing the PDA. Luckly I did a sync before all this happened and I decided to enter a fictional flight to see if it would sync and it didn't. The schedule importer still works though.
There are folders with 6-8 digit identifiers, my suggest is rename them so they will be recreated by your device and not have a problem with overwrites if you have a sync issue. I want to make sure Logbook Pro is pulling in the latest file set from your device to troubleshoot the sync issue.