If you select Edit League Properties and click "OK" with or without changing anything, it removes all players from that league. If you click "Cancel" no player are removed.
You can still see all players until you select another league, upon reselecting the league you realize that no players are in that league.
I noticed in the last update you seem to halfway fix it. Prior to 2.4.2 I clicked "OK" in edit league properties (even if I don't change anything) it removes all league players. Before I clicked on a different league I could still see all players associated with the league. I would then click on a player and an error message generated and I could not edit any players. After 2.4.2 I can select the player, edit the player's leagues (the league edited is not selected) and save changes. I didn't look to see if I could select all players and then add them to that particular league BUT the problem lies in if I accidentally click "OK" knowing that I haven't changed the league and then before reassigning the players into the league click out of that league into another, losing all players and having to manually add every player again.
This doesn't help with leagues that contain a large contingency.