As you’ve found out the hard way, the Prophet X will replace one instrument with another whenever their Bank, Category, and Index # are identical. It really is critical to keep those numbers distinct (at least within each combination of bank and category.)
I have released a utility to safely renumber an instrument after the fact, but it’s currently command-line only. If you’re comfortable with the macOS Terminal or Windows command shell you can download it
here. I really should build a proper user interface around that some day.
... and of course if we can sort out why PXToolkit doesn’t like the .wav file you ran into problems with, you’ll find it has a very different approach to generating index numbers. It will recommend the next number for the target directory, but you can choose any valid number you like (and it will warn you if your choice overlaps with another file in the same directory.) Your choice is saved into a .pxinstrument file along with everything else.
Have you had any luck uploading the problematic .wav?