Sry to dissapoint you, but nothing special happened after logging out, closing the browser, restarted the browser and logged into GOG again. Still both entries, no changes.
Also no "new" Wolfenstein 3D entry with a slightly different spelling.
Whatever happened to you and others, it didnt happened to every one with those games in the library.
You are not disappointing me, and I provided fact not fiction. I also said 'might
be as simple as you logging off and then back on again', often it isn't. The GOG Refresh option usually does the trick though.
It did happen to everyone, but some like you were yet to have your library refreshed before GOG added (restored) them back, so it never completed for you in time to see it.
There was never a different spelling for Wolfenstein 3D, certainly not for me, and I still have both Wolfenstein 3D entries in my library with identical spelling. They each just have a different GOG game ID. If you don't see two identical entries for Wolfenstein 3D in your library, then maybe try the GOG Refresh option. Be aware though, it might make other changes to your library, some perhaps unwanted, though they will likely occur eventually. https://www.gog.com/user/refresh
P.S. GOG often leave versions available, so the files are still there, even though we may have lost visual access to them. If you still have the original link, as I do through my GOGcli GUI program, you can still download them, as was the case, and might still be, with a demo GOG removed from our libraries a year or so back. It is a different story when GOG cancel all access, which is what happened for many of us with Wolfenstein 3D, when our libraries got refreshed etc (original link no longer worked).