There is an term - Engineering Change Orders (ECO). That was made especially for your situation.
For example, you have sinchronized pcb and sch. Then you need to change sch. In this case you need to press in "SCH Editor" Utils->Record ECOs. After all changes are made, you press Utils->Export ECOs. You will write all changes in file. After you go to PCB Editor with loaded .pcb and press Utils->Import ECOs. Now your sch and pcb are sinchronized.