It's actually pretty easy and straight forward. Once you do this a few times, it becomes easy, and will take less than 20 minutes. Here is the process:
I will use some extra clamps to set a few stops so that I can rotate the watch. More on this later. I will also place 2 clamps on the lugs to hold the case down to the machine.
Probing using the end mill:
I need to share that fact that having the Additive Aerospace Probe helps for this type of re-setup. First I will use it to check that the part is flat, by probing the Z in 4 or 5 places. Once I am happy with the watch being parallel to the table, I will move to the main bore. Here I will use a trial and error method of centering the cutter to this bore by probing +Y and -Y until the reading is the same (meaning I am in the center of the bore in the Y axis. Then I'll probe -X and +X until in am in the center of the X axis. I will then recheck the Y just for piece of mind.
Now that Z is flat, and I am in the center of the bore, I will move on to getting the top and bottom lugs in line (This step will get the bolt pattern in line). I will then probe a top and bottom lug. If then are not in line, I will lightly tap it to bring the lugs in line. This is where the 3 clamps from above will allow me to rotate the case without losing the X0 and Y0 position.
From here is should be as easy as rerunning the the old drilling program (with a larger drill), and everything should be perfectly aligned.
Feel free to ask, if I didn't make is clear. I hope that you will try it sometimes.
Band? No haha. This is an OLD watch (20-25 years old) that is just getting a new Case, new hands (glow in the dark, which helps with my aging eyes), a Saphire crystal (because I usually scratch the heck out of mineral glass) and a new Crown (because I lost the old one (so unlike me) I will probably buy a new canvas strap, since I find the metal bands to hot here in LALA land.
PS Wish me luck!