From what I know of machining these heads, there are 3 methods:
1) Remove the pre-cups and mill it as you would any traditional aluminum head. Grind (with a sander) the pre-chamber inserts and re-install separately.
2) Put the whole head on a belt sander (NOT recommended)
3) Put the head on a grinder (rotary sanding wheel) with the cups still in.
It depends on what shop you go to as to what they prefer, but options 1 and 3 are probably the best options. Frankly, I prefer option 3, but no-one around here in TN has the proper tools to do it, so I go with option 1
If they try (tried) to MILL the head with the cups still in place, you might as well throw the head away now. The cups are hardened and when you try to mill the head with the cups still in place, the blades rip the cups out since they're too hard to mill. If the blades hit the cups, chances are the cups got yanked out, and did damage to the their recess in the head. Once that happens, you'll never get the cups to stay in there, short of filling (welding) the head, and re-milling it for the cups.
If the shop did this (milled with cups in place), you should be able to get them for a new/replacement head. If they did not know to take the cups out before putting it on a mill (with cutting blades), then they had no business working on your head, or claiming they knew how to. ALL diesel heads with pre-chamber inserts are the same. So, if they're worked on one diesel head, they'd know this.