I know you have suggested that before, but as I already said twice in this thread I do not wish to alter the time stamps of the files. Changing the time stamps might cause confusion later when we no longer know that the time stamps were changed and why. Also it is not the most practical solution to chase down out-of-sync files, especially if the number of files affected would be larger.
In my opinion this should be regarded as a bug in Syncthing. Maybe the node which detects the issue should ask the sender to recalculate the hash? Or nodes could perhaps verify the hash while sending them?
The link below describes dropping delta indexes by changing the configuration version, it seemed to work but did not solve my out-of-sync problem.