Part I
My main observation was that the game didn't pick up enough of indie college players in the first 4 years of the draft because of the highly rated real draft picks. If you have the patience to sim, I'd sim 2017-2027 to completely clean it out.
Part II
You do this by navigating to specific "draft pool" tab in "transactions" for each indie college league on "draft day", filter players by "college players" and delete those so that none of the indie college players drafted by the NCAA-DI are "drafted" from another college.
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