Hey there, that's working as intended. The old mission was removed due to it being unpolished in general and not really in a complete state. It will return at some point. I hope you understand.
Regarding the controller recognition, it may be that the save files of 0.2.10c is overwriting the one from 0.2.1109b but it doesn't go the other way. To fix this simply go to your /Appdata/Local/ folder and rename the folder "ProjectWingman" to something else. However, once you launch the later versions of Project Wingman you'll have to do these steps again.
Regarding SteamVR, it was a part of the default Unreal packaging plugin which I didn't disable. It has since been disabled for later versions.