Typically the cylinder studs do not have to come out for a cylinder to be bored. Most people operating a boring bar have made tooling to accommodate a wide variety of cylinders/bolt patterns (remember, barrels are bored from bottom to top so simple parallels are often all that's needed to pass between the raised studs to provide a means for clamping). There are some cylinders that could present minor problems but it has been my experience that the TRX250R does not.

Removing the cylinder studs is often a tough job. In order to deck the top of the barrel they have to come out. It's always a good idea to spray some thread loosening agent around them, but it often takes a combination of that, heat, patience, a very good stud puller and some good luck to have them come out well, quickly and without damage or without damaging the threaded hole. With some engines it's not uncommon to always have to replace them, while others seem to "pop" right out. The Snap-On stud puller is the only one I know of that can consistently remove studs without any sort of damage from it - it's literally a four jaw threaded collet with threads to match the stud being pulled, though it takes more time per stud. There is still the possibility that the threads in the aluminum barrel will come out with the stud though it's fairly rare.

It might be best to find out ahead of time (before you remove them) if stud removal is really necessary and if so, why. If the shop insists on taking them out their equipment may be outdated, not tooled well, or it could just be the operator with the same flaws. In other words find another source for the new bore.

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Pulling Studs