Fixing assemblies that have both components and assembly features

OK, so I've learned painfully that Pro/E used to regenerate an
assembly according to the model tree. So it would regenerate fine if
you assembled component A, assembled component B, then made a cut
within the assembly that trims material off of both. This is logical,
after all. It works very nicely for showing the machined form of a
weldment, where you have components to represent the raw pieces and
raw weld shapes. It worked very well back in 2002 or so when these
models and drawings were created.

Current Pro/E releases will no longer support this. It will open but
not regenerate consistently or correctly. I would just be happy to
retrieve the files and view the drawings correctly but that's not
happening.

I now know that you need to use a subassembly to hold all of the
components, put the subassembly into the main assembly, then apply the
assembly cuts in the main assembly. It makes no sense that this
should be necessary. We are doing it the "right" way with new models
of course, but my problem is legacy models.

Our department has a number of assemblies (including family tables,
etc) built in this manner. Each instance of course has it's own
drawing. Re-doing them would be torture. Does anyone know a way to
solve this problem by restructuring or otherwise fixing things? This
also would need to keep the drawings associated and regenerating
correctly.

Thanks,

David