I replaced all of my merged all of my guest units with join and/or enemy units to free up space for new jobs.
I don't understand this sentence
Today I ran into a problem that I expect will be a problem in the future too.
Specificallly. I changed all of the Gafgarion 17's to Gafgarion 11's and they no longer join the party. Now when I bring the new job that occupies job 17 to Dorter Trade City 2, he deliver's Gafgarion's lines instead. If I don't bring them Gafgarion 11 deliver's his lines as he should. I did not change the unit ID's by the way.
How do I fix this?
I cannot even BEGIN to try to bugtest this... You haven't posted anything script wise for us to look at. I've been event editing for a long time now and what you said there doesn't make sense, simply because events don't work that way.
You need to put the script for the event in quest here.
And while you are at it, post a screenshot of the Unit in question in the ENTD.