After a couple of runs synching folders I decided to check the properties of the folders to see if everything was correctly copied over (folder action is Synchronize). The file count didn't match and of course neither did the total size. I checked the subfolders and noticed that three of them (the larger ones) weren't synched properly. The rest of the folders were fine. So I deleted the problem folders on the external drive and synched again. And now only a small fraction of those folders got copied over even though the destination folder had been completely deleted.
How do I get this thing worked out? I believe there is some sort of file where SyncToy manages the last operations which must be cleared. How do I "reset" SyncToy so it understands what has to be copied?