No. Not at all. Not if it's done correctly. The proper procedure is to measure first. Then, remove a small amount of material from the main cap mounting surfaces.
Once that is done, the align hone or boring bar is positioned so that it removes most of the material from the main cap half of the bore, while barely skimming the block itself.
Doing it in this way affects the crank to cam relationship either very small or none at all.
