To see what I mean, use SyncToy to back up a bunch of files, delete a file from the backup, and rerun SyncToy on that directory pair. It will not restore the deleted file. Recently, I started using a new external hard drive for backup, and the only files SyncToy put on it were those I had changed since the last backup to the old external drive.
A remedy is to delete the files by which SyncToy remembers what it thinks is backed up. On my Windows 7 machine, they are
C:Users[user name]AppDataLocalMicrosoftSyncToy2.0SyncToy_*.dat
(* refers to a soup of hex digits and hyphens.) Don’t delete every file in that folder or you will lose your folder pairs.
For convenience, my start-menu shortcut goes to a .bat file that deletes those files and then starts SyncToy. The Del command needs the option /AH, because those are “hidden” files.