If you actually run the setup with the DJS-1000 as master and the other decks are NOT using sync then nothing is actually synced anyway. So your comment was a bit confusing. However, I think I understand what you are saying. DJS-1000 is master, two CD's are synced. When you stop the DJS-1000 maste sync changes to a deck. If this is exactly what you are talking about then just press master on the DJS-1000 once your next project is loaded....OR if in the mix disable sync on the 2nd CDJ you can manually beat match (if that your thing). From what you wrote, you seem to understand this workflow....it is pretty straight forward. It makes far more sense to me to keep the Sync feature as it since a playing deck needs to control time and you obviously need to stop the DJS-1000.
A possible solution is to load each scene up and use only 16 scenes in your set. This way you can always have the DJS-1000 running. I'd prefer this approach for a 1-3 hour set. COnsider that 16 songs (depending on style of music you play) will last 1 hour (ish). You put 16 projects along with 16 tracks per CDJ and you have approx 3 hours. Besides, depending on your use the scenes don't always have to be different unless you are planning a routine. IMHO routines are nonsense. Might as well record it and mix it with a CDJ then but now we are entering into the subject territory.*grin*