Simulation unable to virtual twin process for 4th axis machining and vise/table machining on table in the same program

I'm working with my VAR, but I'd like to leverage the power of this community to hopefully gain some insight.  I have a very common process that we do:  machining on the 4th axis rotary, then an additional set-up in a vise on the same table, in the same program. If I do all of the work on the rotary and then add the vise set up as a "SET-UP", then the vise part will move with the indexing of the rotary, even though it is mounted to the machine.  Weird, why does it ignore the mounting hierarchy of the vise being mounted to the machine?  I expected the vise to stay put and just the items mounted to the 4th rotary would move during the machine instructions.   Therefore, I made it a second part operation....but then it's separate and I don't get a full simulation of both processes.  When I simulate one, it hides the other and we gain no insight on what the machine will do in between movements from rotary to and from vise with regard to clearance and clashing.  This is a test part, and the actual machine has a bunch of pneumatic equipment in between the rotary and vise (that I plan to add later), so clearance issues are VERY common.  We tried sequencing, but the visibility and display of the parts, machined stock and material removal is inconsistent and buggy.  This software is so powerful, there has to be some options where we can gain a complete virtual twin of this process.  Do you guys have any insight?