I did some testing with this the other day. They only disappear if you assign said player to an AHL affiliate or change who owns them. Ironically, you can give an NHL roster as many players as you want (as log as you're under the 50 contract max) prior to starting and they will all show up in your Be A GM. I did this with Florida and it seemed to work out fine. Added a few players from AHL teams and sure enough they made the transition into Be A GM. However, I was running into crazy disappearing acts if I made moves between AHL teams or sending down players to the AHL. I've found it only works if you bring players up, regardless of roster size.
Once you're in Be A GM, you can send them down and retain their rights, trade them, or make space on your roster to keep them and meet the 23 player max.