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First of all, try
rebuild-index command. It will take some time but it will probably fix things.
If it still gives this warning, consider creating a bug report, since Restic should not "lose" the data.
Anyway you can get rid of the error if you can give up the snapshots which are effected by this:
$ restic find --tree XXXXX Found tree 453f9dd1999c9bd89cfd5dd3e574216b6cc0e247da5656ea7d7a19461aeef447 ... path /some/path ... in snapshot br23e8943b (2020-01-22 06:27:20) $ restic forget br23e8943b
This hints there is something weird on your filesystem (expecially with reported X file). I saw this under GlusterFS, which had 2 hardlinks; with same name, under same folder, pointing to same file. Not sure if this is a restic issue, but feel free to ask into restic forum / open an issue to github..