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Not an expert but someone who is doing a similar experiment, circa 1973. I tried a real league with real players, reorganized the teams and held an inaugural draft. Worked great for one year, but when it rolled to the next season all the teams reset to their original cites and names, but carried their new rosters with them. (My San Juan team moved back to being the New York Mets.)
From that limited experience, the Rookie Draft is composed of players who made their ML debuts that year, not players who entered the systems. My guess is you'll either end up with duplicates of all players who were in the minors in Year One then made their ML debut in year 2, or it may delete the duplicates.
If you can come up with a way to pull off what you're trying, I would LOVE to copy it.
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