By default, tracking of moved files is disabled. (Moved files include renamed files as well.) You can enable the corresponding option in the Advanced tab of the sync settings.
When you move a file and this option is disabled, SyncTime will see the old file as removed and the new one as added, so if the file contents did not change, the entire file will be copied again. (If the option “Remove files not on source” is disabled, the file with the old name is preserved along the file with the new name.) This is a minor inconvenience if you rarely move files, since tracking moved files requires the creation of snapshots that occupy additional space (see below).
When tracking moved and renamed files, SyncTime creates a snapshot of the source by storing each file’s path and identifier. Since the identifier of a file always remains the same, a renamed file can be matched to its previous location when the two identifiers are equal.
When enabling this option, the following sync will store the snapshot. Only starting from the sync after that will moved and renamed files be effectively tracked.