Simple ECU question....?

Alright... My civic hatch has a JDM b18C swap. A month ago, my car was broken into and in an attempt by idiotic thieves to steal my VAFC, the wires leading from the VAFC to the ECU were torn and whatnot, and the ECU was stolen. In the mean time, the car has been running on an SI ECU. I now got my P72 ECU ready to go with the right OBD harness and everything. Question is... will switching it throw off the timing, and will I have to get it adjusted? A mechanic told me that since hondas have the timing controlled by the ECU, it might. He might have been talking out of his ass to get me to take it to his shop. I want to make sure I can do this with no problems.. I have having my ride dead in the garage. Also, whats the proper procedure (for switching), I was told just to make sure the - terminal is disconected from the battery.

Thanks guys
- excuse me if its a stupid question.. but im lost in the ECU department :) -

If it's the right ECU, then don't worry about it.

just swap ecu and drive.