This may not impress you but I do small syncs by hand, followed by a big (infrequent) sync with a microsd reader. Of course this doesn't help on the main SD, but I will bet your complex file holdings are on a removable card.
I use winmerge to do the same thing and have the same 'date' problem. Winmerge (which may not be the same) has an option to file match based on size alone. This is good enough for me.