There is no way to refund a game acquired as part of a bundle. While there may have been people who bought the entire bundle for that one game, the fact remains, they still have over 1700 other games.
There are games that get removed from bundles regularly. (I've bought a LOT of bundles, and sometimes discover when I get back to them to download, that some games are missing.) Oxenfree is just the highest-profile one, one that we know is going somewhere else, rather than "creator made Version 2 and removed Version 1 entirely" or "creator got kicked out for bad behavior so their buyers lost access to all those games."
I really, really wish itch.io would provide info about games that are gone - was it removed by itch.io for a TOS violation, or removed by the creator? Has it just been renamed and the purchase is still valid; you just have to find it under the new game or creator name? (Or both. Sometimes both have changed.) And I wish they'd send out notices for games being removed, with a chance to download them - "Creator has removed SuperEliteGame from the itch.io store; you have 48 hours to download it before it's gone forever."