I have done something similar to this by having two sets of clamps and two programs. The only difference between the programs is that one jumps over one set of clamps and the other jumps over the others.
Clamp the part down with one set, and run the correct program.
Install the second set and remove the first set; run the correct program.
It may be necessary to tweak the programs a little bit at the places where they merge. You sometimes get a witness mark where the X,Y motion stops for the Z to lift over the clamp which can be minimized or avoided by having the Z ramp up or the X,Y pull away on a little tangent arc. Then the other program has a ramp down or in inward tangent arc to start. If you are doing a finishing operation such as tumbling or bead blasting it is probably not worth worrying about.
An open mind is a virtue...so long as all the common sense has not leaked out.