sound shift or root

a general question is whether diverging word stems appeared through a sound shift or a duplicated route.
those duplicated roots were quite frequent in proto Indo European vocabulary:
kwerkar (work = kar @ persia)
𓂜 muno- (celtic for no¬ µo¬ negation)
...
todo

it is also possible that those duplicate roots were formed after the sound shift, in order to keep the system together, or to facilitate communication so that one party always understood one part of the word.