Interesting point that occurred to me a while back, but there are no such "chemistry effects" in the game engine, so your players won't be affected by how long they've known their team-mates or how long they have played for the same team. The only thing that may capture something different from the main skills is experience, but players would have exactly the same performance regardless of the team they're playing for.
Selling a player who has been with you for a while may affect merchandise if he was an important player. The item "I'm familiar with the star players..." in the fan survey shows how fans feel towards your shuffling of the roster. Good luck ;)