Only the verb directly referring to the beth will have the mutation. So:
Be dach chi’n trio ei wneud - What thing are you trying to it do.
Be dach chi’n ei drio? - What thing are you it trying?
Also in statements:
Dwi’n ei drio fo. - I’m (it) trying it.
Dwi’n trio ei wneud o - I’m trying to (it) do it
Dwi’n trio gwneud rhywbeth - I’m trying to do something
As has been said elsewhere, the first pronoun is often left out, (but there is sometimes a mutation left over to mark its passing.)