A craniotomy is a surgical operation in which a bone flap is temporarily removed from the skull to access the brain.
Craniotomy is distinguished from craniectomy (in which the skull flap is not immediately replaced, allowing the brain to swell, thus reducing intracranial pressure) and from trepanation, the creation of a burr hole through the cranium in to the dura mater.
These procedures are used to open the skull.

Since your original says: trepanation, you could use "trepanation flap", but that is sort of historic term and I don't think it should be used when describing a recent cranial surgery.
The original text is compiled in a terrible manner, however, there's nothing you can do about that.
It would be better to apply a term which is much more up-to-date (you haven't mentioned what way they're opening the skull), and is related to the nowadays procedure:

Craniotomy or craniectomy flap (depending on whether they replace or not replace the bone flap)

This link might be very useful, please check it out. It has pictures and explanations of these procedures.