I guess from a PX toolkit perspective, as long as I use different folder names than the ones present on the unit then I should be safe?
When installing instrument it will only overwrite existing sampled instruments when all three of the following match: bank, category, and instrument number. The easiest thing is to make note of what banks you currently have samples installed in and avoid those – but in a pinch you can install in an existing bank so long as it's in a category you haven't used before, or in numbered instrument slots within a category that already aren't in use. When installing a sampled instrument that matches the bank + category + instrument of an existing instrument, it will replace the older samples.
The main reason to avoid getting too clever with filling in a bank with a bunch of unrelated instruments is that the only utilities available on the Prophet X to delete samples will delete
an entire bank. There's no way to delete a specific instrument or just one category from the bank. It's the whole bank or nothing, though you can also overwrite specific sampled instruments by installing new ones on top of them.
There's a project for one of you clever programmers!
The Prophet X doesn't appear to provide any external access to installed samples. They treat the factory samples, add-on, and user samples in the same manner from this perspective as far as I can tell – presumably to protect the copyrighted material that forms both factory and third-party samples.