You are missing out on a lot of options within Import Session Data. For what you describe, I would use ISD and grab ONLY the tracks that have the plugins with MIDI control working, and bring those tracks into the other sessions, but DO NOT import the audio(media). Once those empty tracks show up, just drag the plugins from the blank imported tracks and drop onto the tracks where you want, then delete the empty imported tracks
Another option; take the session WITH the control changes working and save that as a session template(again, do NOT include media). Create a new session from this template and import the audio files. I'm sure there's more options I haven't come up with too
