Not sure if I'm understanding the issue properly, does it seem to be captured in the Idea noted below?
If so, please feel free to up-vote it (so that it becomes more likely to be included as a feature)
Why not build both flows in one packaged flow? You could simply separate the two flows with space, and use two separate flows in the same packaged flow file.
I hope this helps -- certainly, you'll want to avoid running multiple instances of Prep, unless you have LOADS of memory -- stick with one prep instance at a time. I try to do the same for Desktop (only open one packaged workbook at a time).
A lot of the miraculous stuff Tableau does happens in memory, so it can be a balancing act to find what you want - let me know if you can just build both flows into one flow pane (it is definitely possible)