Looking at a test VM the problematic files seem to be present in the read-only base but then have been at some point deleted. So when the rename/move is attempted there are whiteout softlinks present in the overlay.
E.g.: /media/root-ro/var/lib/cloud/data/status.json /media/root-rw/overlay/var/lib/cloud/data/status.json -> (overlayfs-whiteout)
#> cd /var/lib/cloud/data #> touch tmpfile #> mv tmpfile status.json mv: cannot move 'tmpfile' to 'status.json': Stale file handle
Looking at a test VM the problematic files seem to be present in the read-only base but then have been at some point deleted. So when the rename/move is attempted there are whiteout softlinks present in the overlay.
E.g.: root-ro/ var/lib/ cloud/data/ status. json root-rw/ overlay/ var/lib/ cloud/data/ status. json -> (overlayfs- whiteout)
/media/
/media/
#> cd /var/lib/cloud/data
#> touch tmpfile
#> mv tmpfile status.json
mv: cannot move 'tmpfile' to 'status.json': Stale file handle