I have a similar issue. Let's say you have an SD card that you use with a camera, and you just want to "Contribute" the files to a backup location with SyncToy. From time to time, the card may get re-formatted. Rather than give me the message "Failed to
execute folder pair: This folder pair cannot be synchronized because SyncToy cannot find the correct marker file in the folder <xxx> to <yyy>. Please recreate the folder pair if this is the correct drive and folder to synchronize. <OK>"
I believe that if the action is "Contribute" and the marker file is missing from the source only, SyncToy could instead (1) give me a warning like the above, and (2) give me the option to proceed and overwrite (ie, recreate) my destination marker and create
a source marker.
Normally, I wouldn't remove the marker from the source SD that the camera uses, but the last camera firmware update said it required reformatting the SD card.
I don't have as much work to redo as jadocja but it is meaningless work because I am recreating exactly the same folder pairs. It's only complicated in that I use include/exclude to sync my camera pictures with one folder pair and sync my camera videos with
another folder pair.