For PaperUI discovered Things, you can backup the /var/lib/openhab2/ directory.
In there, you will find the jsonDB (in folder /var/lib/openhab2/jsondb) where OH2 stores (and creates and autobackup) your Items, Links, Things and other stuff that you manage via the PaperUI.
For manual configs, backup the /etc/openhab2/ directory.
Most likely: filesystem corruption that affected your /var/lib/openhab2/jsondb/org.eclipse.smarthome.core.thing.Thing.json file (check to see if it’s still there and if it’s readable. If yes, copy the contents, delete it, recreate it and paste the contents back).
It’s highly unlikely that a system update would wipe out your json database.