There is no reason why this will affect the Challenge Cup, as the RL only uses it one day a year.
Presumably, if sold, then Wembley will be leased as a venue by the new owner using a couple of potential commercial models to the RFL:
1. A contract for x years, to hold the Challenge Cup Final at Wembley at a cost of c£1m pa. The RFL then market the final and profit on all revenue less this lease cost, ticket contributions to clubs etc. This will be similar to the deal what the RFL have currently with the FA.
or
2. Wembley bid, along with other stadiums, to host the Challenge Cup Final each year. The RFL receive a fee upfront and then the venue markets the event keeping all revenue. This model is similar to Test Cricket, with each Test ground bidding against each other to host the Ashes Test matches. The ECB get a guaranteed revenue up front and then its up to the venues to worry about ticket sales, weather, how long the game lasts.
With the second option, the RFL could use the opportunity to allow other venues e.g. Millennium Stadium, Old Trafford, Murrayfield, a new Odsal, and New Craven Park
to bid for the final, therefore driving the fee up. Presumably, the RFL would then pay the competing clubs a share of the spoils.