My 2c:
It is ALWAYS much easier, and usuallly far more accurate, to use the original program to make a machining jig. Once you have the jig made, as OP have said you clamp the part onto the jig and continue the program to add the extra holes.

I often add a small detail to the jig: a straight machined (front) edge on the X axis and a bit machined off on the Y axis. If I have to repeat things, I can always mount the jig square and clock off the corner. I can do that with just a shim gauge and a known rod in the mill chuck (frequently the shaft remains of a broken 6.00 mm carbide end mill...)

Cheers
Roger