The typical case is probably that someone (like me) has all branches of Pike checked out at the same time:
cvs ci -m 'Fixed something or other.' */path/to/patched/file
If the patched file hasn't diverged earlier odds are that the new file will still be identical accross the branches and have identical history.
I always wondered how this was done. This would explain it. Then we have no business messing with merges here, simply make a clean split and keep the branches truly separate after that.