I think this is just a Sphinx thing where the phonetic dictionary isn’t being changed since there is already a phonetic dictionary with that name, and then you have a phonetic dictionary with different work contents than the DMP (not corruption, but also not possible to make a match when a word is spoken). IIRC from past development in this area the API for changing a model set is a little more straightforward than the API for changing the phonetic dictionary contents and what I have in there might not be as resistant to unusual situations.
My recommendation for an approach that shouldn’t cause any user-apparent time overhead or file system clutter is just to have a method which appends an incrementing int to the end of the chosen file name and deletes the one with the previous int ending.