[mitchkenn]

if you go to league settings> leagues & teams - on the far right is a drop down box, probably says Major League Baseball ML .... if you click on that you will see your minor league levels. If you pick, say AA, it will show all the teams that are in the system. It will also tell you if they are affiliated with a team or not. The teams with no affiliation, their players are free to be signed by any team.

if the Team loses affiliation, the players become Free agents.

unfortunately, real teams changed affiliations from time to time, and the game reflects those changes, so i don't know a solution other than checking before each season what affiliations you have. i suspect in future patches or version, they will smooth this out. After all, this is the first year for historical minors and it's been a major undertaking. I'm amazed at how well it does work, even with some hiccups. (i started to amass my own minor league data base once, so i could get around those disappearing affiliations ..... and was so overwhelmed by the sheer size of the project, i folded after two weeks.)

if you want players to go to the teams they actually started in, you need to have BOTH of these - check the box that says Automatically import historical rookies & have the draft turned off (draft can be turned on/off only in off-season). If you have the draft, all the players go into the rookie draft, not the teams).

don't think from your write-up you have your own minors, but they are NOT compatible with the game if you have historical minors checked. Those teams will vanish at the end of a season (every season) and players end up free agents. (i've tried various methods to get around that, to no avail .... maybe in future versions, but for now.)

not certain this addresses your exact issue, but it's a quick over-view of what could be happening and some things to look at or avoid... Hope it helps.