It was fun while it lasted!

Did you put the card in laptop while backing up? The same thing happened to me, I backed up using laptop SD reader, then Thing settings got cleared when put back to RaspPi. You can look for backup under userdata/jsondb/backup folder. Core files:

org.eclipse.smarthome.core.items.Item.json
org.eclipse.smarthome.core.items.Metadata.json
org.eclipse.smarthome.core.thing.link.ItemChannelLink.json
org.eclipse.smarthome.core.thing.Thing.json

Move good backup files from backup folder to its parent folder, remove time stamps from file names. Do this when OH service is stopped.

This might have something to do with file access times being modified by laptop’s OS, then later jsondb in OH finds them inconsistent with its last known house kept values, and decides to reinitialize those core json files. But backup will definitely be there.

The issue is valid though, need a ticket on GH. OH SD card when put in laptop, file systems mounted, copying done, put back in RaspPi, Things and their settings are gone.