I had the same problem with my Nextcloud app. It seems the issue was in the nextcloud-pre-upgrade1.info.json.
The from_yunohost_version was set to “0:”. I just changed it manually to “4.2.2”, and ran
sudo yunohost backup restore nextcloud-pre-upgrade1
and my app was back.
I hope that it can solve your problem.
Edit : I don’t know how to solve the upgrade issue