Synchronise generally means copying the latest version of the file to the drive that doesn't have it. Usually that's based purely on time-stamping, so it can produce some odd issues when the clocks change if you are using FAT rather than NTFS.
Generally, the move will take place from C to the external drive, leaving both drives with the same set of files.
The thing to watch, though is the clock change issue, which changes the 'apparent' time of files on a FAT drive. This can result in them all being transferred to an NTFS volume when you sync, because NTFS stores an absolute time, whilst FAT stores a relative time.