I amusing the Halion SE instrument in cubase and am dragging biab plug in generated tracks into my cubase program. The real tracks make wave files, no problem, but the midi files come over, and the midi insturment sounds get mixed up. guitars in biab become violins, strings become other crazy 'goblin' sounds. When I try to reassign the midi sounds in cubase, they won't 'save' as the correct sounds, ie guitar or strings. Every time I go back to the beginning of the track the reassign to the messed up sounds that came with the midi file. any ideas?

Delete the Program change in the midi file.

This can be done using the Event List in Cubase:

https://steinberg.help/nuendo/v8/en/cubase_nuendo/topics/midi_editors/midi_editors_list_editor_event_list_r.html

Find any Program Change or Patch Change messages (as well as any bank select messages, if Cubase separates those from the program change) and delete them. I'm afraid I can't be much more specific, as I do not have Cubase available to test on.