Your workflow seems back-to-front to me
I'll try to describe this in a simple way.
Can you not have one parent part? (e.g.part1.ipt).
In that parent part have just your base features,
say, an extruded circle.
Then use that part to derive two new parts
Use Part1.ipt to derive Part2.ipt and put fillets on it,
(ie the features you have in your complete part)
Use Part1.ipt top derive Part3.ipt and put other features on
it.
You will have to strip out (suppress\delete) the features on
your parent part down to the state that is acceptable for your new part, but you
could use copy and paste from the original to recreate the
features.
Sorry if this is not clear, but I guess you are asking for a
wish. That is to be able to suppress Part features in the derived part
dialogue.
--
Best Regards
Richard Rankin
Autodesk
Manufacturing Solutions (Support)