The demographic/patient ID will not overwrite any data. Basically, from what I have been able to ascertain, the AC you are doing the syn from has precedence over the AC database that you are importing to it. This is true whether you are merging data or adding remote updates.
So, if your current database had its first four patients as 1000, 1001, 1002 and 1003 and the new database had the same, then if you went to the admin section of the current AC and updated from the new database, then the new databases 1000 through 1003 would become 1004 through 1007 and vice versa.
I believe if you do the syncing from within the current AC, you will be OK.
Personally, I would move the server folder to another computer and sync the database with the newly imported data over. Just play around with it until you know it is right.
