not exactly sure what you want but if you wish have R1, R2 and L stay your preferred instruments and different instruments to those in the midi files no matter what midi files play in medley:

you don't need any software or to edit anything in the midi files. Just go to midi menu, mode setting, and choose gm 2 with channels 1-16 = parts 1-16.

if you now direct play a medley of midi files R1, R2 and L are independent of all parts playing in the midi file and will play whatever instruments you choose, and will stay these instruments no matter what midis play in the medley.