I haven't dug through enough of the MM code, but what appears to be happening is that the server is resetting the game (which clears all the entities) when it enters the victory phase, while it used to do it after the victory phase ended. Since MHQ processes the scenario when it receives a game change event that indicates the game changed from the victory phase to another one, it can't find any entities and marks them all as a total loss. The exception is an entity without a pilot, which is marked as crippled but I haven't looked into how MHQ gets the info that the pilot is missing.