umm, i think the point to doing this is so that the car does not loose memory, form either the ECU or other components like Radio.
If you have your radio security code(Or an after market H/U), the I would not bother with the 9V.
Once you bolt the engine up again with small changes, the ECU will need to adjust to the changes you made, so by disconnecting the ECU, it will have to reset itself anyway.
In other words, should be no problem.
CAUTION: Slippery When BOOSTING!