you can do an IN clause in your FilterClause, e.g., CustomerId IN (Select CustomerId from CustomerIdsTable where ClientId = @ClientId)
however, please note that Sync Framework doesnt support "partition re-alignment" or rows going "in-scope" and "out-of-scope".
Assuming your client initially has customer Ids 1 and 2. The you change the filter so that the customer Id list is now 1 and 3. The previously downloaded data for customer Id 2 will not be removed from your client (these rows just went out of scope). Likewise,
unless the rows for customer Id 3 has been updated since the last synch, they will not be downloaded by your client (these are rows are going in-scope).