Probably not unless the jailbreak is removed and the iPad restored.
I think that's how it was with previous upgrade.
not sure if you are misunderstanding question. You will be able to upgrade your JB iPad to 4.2 . You will just lose your JB. This is what happens all the time on iPhone and people then say "I upgraded by mistake to 184.108.40.206 how do i JB?"
As said by nooris if JB is important to you don't upgrade until a stable JB for 4.2 has been released.