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)
Reason for having 2 packaged flow is to keep a change control, one flow in production which is been run daily and the other "copy" of production is worked on by developer. However the developers often have to open both versions and even it is possible to open Prep twice it often takes up all the computers memory. Honestly, unlike Alteryx where you can have 2 flows in the same application/window, Prep would have 2 windows and computer with low memory - it is just bad user experience more than anything else to be honest!