I believe this is due to the same files have different modtimes on the source and destination. That’s fine I just use checksum. But after running a full sync with --checksum I expected rclone to update the modtimes on the destination so I don’t need to use checksum anymore, but it did not.
Yes, no dupe issues. It’s definitive not updating the modtime when finding a match with checksum doing copy or sync. Running this modified version (Only update mod-time without copying file) fixed my differentiating modtimes for now but I think the official one should do it as well.
Sorry, I misunderstood what you were saying - I thought you were worried about the different number of checks in your first posting.
As you noted running with --checksum doesn’t update mod-times - it only checks the checksum and ignores the mod times completely. This is because reading mod times on some remotes is expensive (takes another round trip) so you don’t want to do it by default.
