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I think it is just that file, but there are others more knowledgeable than me about the minors in OOTP. As a rule, the less you edit, the better, in case it does crosswalk to other things. Maybe just change the affiliation column from IND to the abbreviation of the teams you want to have affiliates. In either case, backup the game and save an unedited version of the file to put back in case this go off the rails.
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