The logic that I can 1st boot up the PyTrack ... get a usb-serial port ... then I hot-swap in the FiPy ... the FiPy boots up ... means there is enough voltage / current for it to boot up ...
Why the issue dissapears when I attach the LiPo Battery, and get a usb-serial (too) is key.
Actually what @robert-hh is saying lines up rather than your logic. Booting 2 devices together at the same time will have a much higher current spike on boot up rather than powering one device then the next as after the initial boot current draw will drop. Also a lipo battery can supply more current than a standard usb port. For instance most 3g/ lte modems spike above 500ma on send and can fail when using a usb port on their own.
Again you could be right and it's not an issue but the symptoms you're seeing with the fix you have point towards a current or voltage issue.