Retain MIDI input settings when replacing instruments?

Here you are - install Duplex, then copy the attached file to the Duplex/Controllers/ folder (overwrite the existing mpd32 folder)
Note that you can open the tool folder by using the tool browser: right-click, View in Explorer/Finder etc.

If you are using the standard layout for the mpd32, you should have 16 pads that you can route to whatever instrument/track that you would like.
These settings are kept between sessions, but not saved per-song (that might be a useful addition in a case like this)