At the start of the season, you have to subtract 14 players (40 man Spring Training roster down to active 26 man roster) which then subjects those 14 players to optional waivers, if they have no player options available. That is why you're only losing some and not the entire roster.
At the end of the season, I'm not sure since you stated that all players are signed to 15 year contracts.
The best option for you would likely be 30 team control so that you can manually control all teams rosters and therefore, if something were to happen where a player were to get removed from the team, you could simply add him back on.