Not if it's done correctly it won't change a thing. The correct procedure is to knock a little off the main caps where they meet the block, then assemble and torque them to spec in place. Then set it up on the bar and BARELY clean the block side up while taking the most material out of the caps. Doing it this way will change nothing concerning the timing chain. I've even seen shops lightly spray paint the crank saddles in the block so they can remove the absolute minimum from the block side. If the shop refuses to do it that way, find a new one.