This can happen if you have the "Prevent AI Roster Changes" option enabled for your minor league teams while at the same time having your minor league teams set to AI control on each GM's Manager Options screen (in layman's terms, the logical impossibility of asking the AI to control the minors while simultaneously telling it not to make any changes to the minors causes it's head to explode).
You can disable the Prevent AI Roster Changes option on a league-wide level from the Functions tab of the League Setup screen, though you will need to do it for
each minor league. After that, simming another day should "restore" the seemingly-missing players.
I'd suggest you try that solution with a clone/backup copy of your league first of all, though, since advancing the game date will require online GMs to download a new league file before they can export again.
Let us know if that doesn't solve the problem.
- Kai