If the same size is used, shouldn't be a problem. You may find the existing drywall in the light shaft is a bit mushy, you will want to replace it, if it is.
We don't know how the existing drywall is, in relation to the actual skylight. There's a lot of "if's" involved, at this point it would only be speculation to give you a yes or no answer.
Velux lights have the interior of their light, where it can be stained etc, or drywall ran up in side to a channel in the wood. You can have the finish appearance of stained wood, then put a thin trim boxed out at the top of the drywall. You may be able to do this, only someone who knows how your existing is done, will be able to tell you. And, they may not until they get into it.