I've removed tons of the studs and never ruined one. I usually can get them out by double nutting them but have also used a channellock multiple times. If you use a channellock (about a 430 size works well) grip it close to the body of the saw. It will screw up the threads some but guess what? those threads aren't needed as the bar and clutch cover extend past that area.
You'll need a good quality T-27 Torx (I use one with a drill driver as it really speeds things up) Hand torque the reassembly, not with a power tool.
An impact works well to take the clutch off. (I use an air driven 3/8 butterfly) remember it's backwards threads on the clutch and regular threads on the flywheel.
To remove the flywheel, I loosen the nut with a 1/2" 3/8" drive deep well socket. (it's 13mm but the 1/2" fits a little tighter) Then I hand screw the nut back down and then back it off about 1 full turn. I then get a good grip 0n the base of a flywheel fin with a pair of duck bill pliers and holding the saw a couple inches off the bench I give the socket a hefty whack with a 12 oz brass hammer. One hit will typically loosen the flywheel.
On reassembly, I put the engine together, let it sit overnight and then pressure test it the next day before I assemble the engine into the engine housing. (it takes some spacers/bushings to take up the bolt length)
Everything else is undo what you did previously. If it's an aftermarket cylinder, many of these have the wrong size hole where the coil wire goes onto the cylinder. Use a #10 coarse screw in this spot.
Be sure to install the impulse line on the new cylinder before you get it all assembled as it's hard later.
Yes, retune when finished and go cut wood.