Are you playing a Historical simulation? That's what I play, and I can tell you that minor league teams occasionally do come and go. My very first season as a GM was 1981 and when 1983 began I noticed that I had lost TWO of my lower level minor league teams. I did not lose the players, however, they were just thrown onto the roster of a different minor league team of mine. 1984 came along and I got my lowest level GCL team back.
If you are ever curious, baseball-reference does a great job of listing even MLB club's minor league affiliates throughout the years. Here is the page for the NY Yankees:
https://www.baseball-reference.com/r...ate.cgi?id=NYY
Take a look at their minor league teams for 1948. Yup. That's right... 24 minor league clubs. Crazy...
If you are playing anything other than Historic, I can't help you there...I've never played anything but Historic. Good luck!