Hey Tim,
When the app is deleted, the database is lost - so we can't recover your waypoints or map tags (the names you gave your map downloads and the date downloaded). The map image data is still there (which you observe), so Gaia will use it in the usual fashion - but your maps won't show up in your saved maps list.
We think that moving the database files to the SD card will be a performance issue, because SD card read/write is slow. I can see why it's problematic when flashing your ROM though.
While we can't address this immediately, could you put a note on our UserVoice forum so others can view, vote, and comment?
gaiagps.uservoice.com
I'm sorry I don't have a better answer now.
Regards,
Andrew