With a missing tree, prune will fail hard (see below), new backups are fine. rebuild-index did not complain, but did not fix the problem.
If the corruption is persistent and confirmed, how can the repository be “repaired”? I expect there will be data loss, but can the structure be repaired to a state were prune will succeed (or does purge need a fix so the error is non-fatal)?
I reviewed the suggestions from Persistent repository corruption and data loss, and one extreme solution would be to forget the affected snapshot.
$ restic prune
repository a7073830 opened successfully, password is correct
loading all snapshots…
finding data that is still in use for 70 snapshots
[0:00] 1.43% 1 / 70 snapshots
id 004d3d7d3c7619f9aa7c02e53d62bbc007d7f3ee47e2676714c32360fbce121f not found in repository