Mute automation and muted clips do not affect exported MIDI. As long as a MIDI track is not muted by clicking its Mute button, or an Instrument track is not muted by clicking its MIDI Mute button (Instruments view), all of its MIDI data is exported.

When exporting MIDI files from Pro Tools, device assignments for tracks are not retained (though channel assignments are). If you export MIDI or Instrument tracks from Pro Tools and later re-import them, you will need to reassign the tracks to devices in your studio.

All timeline location information of clips on MIDI and Instrument tracks is lost when exporting. For example, tracks that previously contained dozens of MIDI clips will be flattened and only contain single clips after exporting and re-importing.