It's not recommended to switch from moly to non-moly shooting. Though, if you DO, you don't really need to be all that worried about getting all the moly out of the bore. Those stories come from the benchrest crew who lose sleep over 1/4 MOA. For the rest of us, I doubt there'd even be any noticable difference, especially after a few boxes.
JB is probably the easiest way to remove moly, if you decide you absolutely must get rid of it.