Sorry, yes, the one area we did change the pinyin was undoing sandhi transformations like this since the convention in dictionaries is not to show them; instead we show the unmodified pinyin but then play audio with the correct pinyin. Following that convention means that words will match up correctly with the pronunciation in most of our dictionaries, which in most cases means fewer duplicate cards rather than more of them (i.e. if you added bu4yao4 manually from a reader lookup).
bu2yao4 should not match anything, but in your case seems to have matched an entry in Tuttle because they happen to be the one dictionary in our bundles that doesn't follow that rule (though we're planning to fix that). If you didn't happen to have that dictionary installed, it would have fallen back on a dictionary where the pinyin didn't match and picked up that bu4yao4 pronunciation anyway.
Basically, neither entry is incorrect, the approach in the new file is a better fit with the rest of Pleco going forward, but if you prefer not to deal with that change you can import that other file I uploaded and that should preserve your existing cards.