I added to and moved some folders in my filesystem inside folders indexed by Digikam, but Digikam is not finding the news one and is showing the moved ones in their old location. I tried refreshing the album and scanning for new pictures, but neither worked. If I right-click and select "open in file manager" it show the correct folders (which isn't suprising since that is just the underlying filesystem). Does anyone know how to fix this?

I am using digikam 1.3.0 with KDE 4.5 on openSUSE 11.3.

Can't confirm (though running Digikam 1.3 under 4.6svn). Moving folders indexed by Digikam didn't cause any issues, moved folders showed where they should. Corrupt db or collection settings?

If that was the case, how could I fix it without losing my entire collection?

Won't the collection just be repopulated if you deleted the db?

Yes, but will my tags be there? I know some have been written to the files, but I am not sure if all have been. I am also not sure if the tag hierarchy will be preserved. I guess I could rename the database and see how things turn out.

I did a little test and it appears tags would be lost

You know that in config -> MetaData -> common MetaData actions it seems you can automatically (?) have the tags saved to file instead of periodically using tools -> write MetaData ? Or have it stored in Nepomuk?

Yeah, I already had that set, so the tags were retrieved when I made a new database.

If matadata was written to files tag hierarchy will be preserved on import (saved in XMP).