I've had a go at implementing the --refresh-times flag here
https://beta.rclone.org/branch/v1.52.1-077-g21dec334-fix-1505-refresh-times-beta/ (uploaded in 15-30 mins)
Feedback appreciated!
--refresh-times
The --refresh-times flag can be used to update modification times of
existing files when they are out of sync on backends which don't
support hashes.
This is useful if you uploaded files with the incorrect timestamps and
you now wish to correct them.
This flag is only useful for destinations which don't support
hashes (eg crypt).
This can be used any of the sync commands sync, copy or move.
To use this flag you will need to be doing a modification time sync
(so not using --size-only or --checksum). The flag will have no
effect when using --size-only or --checksum.
If this flag is used when rclone comes to upload a file it will check
to see if there is an existing file on the destination. If this file
matches the source with size (and checksum if available) but has a
differing timestamp then instead of re-uploading it, rclone will
update the timestamp on the destination file. If the checksum does not
match rclone will upload the new file. If the checksum is absent (eg
on a crypt backend) then rclone will update the timestamp.
Note that some remotes can't set the modification time without
re-uploading the file so this flag is less useful on them.
Normally if you are doing a modification time sync rclone will update
modification times without --refresh-times provided that the remote
supports checksums and the checksums match on the file. However if the
checksums are absent then rclone will upload the file rather than
setting the timestamp as this is the safe behaviour.