It might make a big difference to know whether the league in question is a historical league in which everyone has the opportunity to know the full trajectory of each player's career, or a contemporary league in which trades to the other league aren't known until they happen in real time.  If it is a historical league, you could do what an old tabletop league of mine did, and allow owners to retain the contracts of a certain number of players who disappear from the league universe (for any reason) and then reappear in a future season.  In that league, which was 1930's-1940's AL-only, we were allowed to keep up to 3 players who were temporarily unavailable.  Such a reserved player could be released or traded while the owner was waiting for him to become part of the player universe again, as long as the total on each team didn't exceed the limit. For players who disappeared from the league universe permanently due to trade, they were treated no differently from players who exited the universe for any other reason (death, injury, old age, etc.).  Presumably the owner knew, or should have known, when it was going to happen at the time he acquired the player, so the cost of investing in the player reflected that fact.

For a contemporary league where interleague trades aren't known in advance, you could allow the same type of reserve system, which would allow the owner to reclaim the player if he ever comes back into the league you are using.  Or you could just treat it the same way you treat deaths, injuries, sudden losses of effectiveness, the discovery that a player is playing under an assumed name, or anything else that causes an owner's investment to suddenly vaporize.  I am in 2 Rotisserie leagues, one AL-only and one NL-only, and that is how we treat interleague trades.  A few years ago one league owner had the very valuable #1 pick in the minor league phase of our NL draft and used it to pick Oscar Taveras.  We don't have any provision to compensate him for the sudden and unexpected loss of Taveras due to his death.  Should a sudden and unexpected trade be treated any differently?

Actually, in our Rotisserie leagues, the prospect of moving to another league is something that does (or at least should) factor into the auction price of the players.  A key player on a likely contender in the prime of his career is less likely to be traded in the near future than aging players on noncontending teams, young players on a crowded depth chart, or players who don't get along with their management.  To some extent the market adjusts for those different probabilities.  With Derek Jeter in his prime, you knew he wasn't going to be traded any time soon so his league value reflected that.  On the other hand, in my AL league I have Mookie Betts, who looks like a legitimate major league hitter who could be very valuable for a long time in the right circumstances, but who will be fighting for playing time in Boston's crowded outfield and could find himself traded to some NL team next summer.  If I try to trade him, his uncertain future with Boston will really drive down his price.