Relevant quote (regarding the ability to replace a file with a new type or bitrate) from my last comment from duplicate #51.
I should note that this will result in the beatgrid, hotcues, and hotloops to be off due to the different bitrate. Correcting for this is much more complicated. If I do expand Tuneup to offer Denon to Pioneer conversion, the groundwork required for that will make bitrate conversion much easier to add. Until then, changing the format or bitrate of a file will require a re-analysis. I could potentially include an option to clear the beatgrid and such to force a re-analysis in these situations.
Relevant quote (regarding the ability to replace a file with a new type or bitrate) from my last comment from duplicate #51.