How do you design mating machines without cyclic references?

My company designs coil processing equipment lines which is a progressive series of machines that unwind, flatten, cut and stack steel coils into shaped blanks. With this being a series of machines, it is important that they all mate up properly to one another. The way we've accomplished this for the last 15+ years in solidworks has been to show the mating machine before and after every machine.  So machine 2 has machines 1 & 3 in it for reference purposes. Machine 3 has machines 2&4 in it. Etc etc all the way down the line. This way we can show on our 2d layout drawings all the interfaces of each machine.

This year we purchased EPDM and as we are approaching our rollout and doing debugging, we find that EPDM won't allow this type of cyclic reference. This seems to be a deal breaker for us but we already have such a large investment in the software. How do you get around an issue like this?  We can't be the only ones trying to show mating equipment as references in assemblies.  This seems like a critical aspect of designing total systems that was completely overlooked somewhere, or we are just too set in our ways to see outside if our box for the solution. Your advice is greatly appreciated.

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