I'm not sure if this is what you are looking for but I'll try.
Are you using a sequencer like Cakewalk?
If so, load your midi file and look under the INSERT function in the menu bar. You can change the file into any Key signature you want. I would then 'save' it as a revision of the original so that you could 'go back' if needed.
I use Master Trax Pro Audio and it also has a key change function. (I think they all have.)
Is this what you need?