Judging from the background story in Very slow restic prune , my guess would be that the S3 bucket listing is incomplete from time to time. So, a quite likely explanation is that the list of pack files which prune gets in incomplete and hence the missing file errors. As far as I remember, minio has options to ensure a consistent file listing or maybe you’re encountering some timeout.
Is there any structure visible in the pack file names reported as missing?
Please do not open a new topic when there’s no quick reply. It doesn’t help to loose context when taking a look at a problem.