Probably, but re-jetting would be determined by the difference in the amount of restriction each system has. Changing from 4-4 to 4-1 or vice versa, or to open pipes, changes the restriction a lot so re-jetting is usually required.
In your case, if the systems are similar it shouldn't be a problem, but if one of the set-ups has significantly more or less restriction it might be necessary to re jet (ie, if one of the systems has had its baffles removed etc). In that case you could just try to swap the header section and keep the muffler, since the difference in the headers should be pretty minimal (but that probably defeats the purpose if the pipes are that different...)