3D Realms have posted a news update for customers who bought the game through the (now apparently defunct) digital download service, Triton:
2K has set up a replacement program for customers who purchased Prey via the Triton download service. A new boxed copy of Prey will be shipped to each customer who purchased the game via Triton, DiStream or http://www.playtriton.com, as Triton is undergoing a reorganization process and copies downloaded from the service may not function properly. There is no action required on the part of the purchaser. Boxed copies will be mailed automatically to the credit card address on file. Thank you for your patience during this interim period; we look forward to getting affected customers back up and playing Prey as soon as possible.
Whatever’s going on between the companies involved, it’s good to see 3DRealms making sure the customer is taken care of and kept as happy as possible in the circumstances.