Replicating data to a head office with limitations
You might be able to do something with actual SQL replication, but if you've already got an existing routine, just modify it to filter specifically on a new bit field in every table: uploaded or whatever you want to call it.

So when the register writes the changes to the table, make sure it clears that bit. Or, if you can't alter that part of the routine, put an ON UPDATE trigger on the table that clears it when a row is updated.

Then make sure that the "upload to corporate" routine sets all those bits when it copies the data up. 

Or, what might be even more useful, is to have a "last changed" field updated by your register uploads, and a "last uploaded to corporate" field. That way you can compare the two.