I see that there is still some confusion about how the original version of Spear of Destiny disappeared from anyone's library, even if they had bought it the same day it was released.
Let me explain to the best of my ability the technical flaw that allows this to happen, but first we need to step back and take a look once again at how GOG handles games in its store.
In the GOG store we can observe three types of digital goods that can be purchased:
1. The actual games, these are the assets that end up directly in your private library once purchased and increase your counter of games owned. On GOGDB they are classified simply as "Games" and each has a unique ID.
2. DLCs, which are files that are added to games you already own, they don't increase your games owned counter and aren't purchasable unless you own the game on which they depend. On GOGDB they are classified simply as "DLC" and each has a unique ID.
2. Packages, which we can imagine as the wrapping paper that envelops a bundle of games and/or DLC. When you buy a Deluxe Edition or Bundle on GOG, you are buying a package that contains the game and the various DLC extras. The packages themselves don't appear in your library, and you can only find them mentioned in your order history. On GOGDB they are classified as "Package" and each has a unique ID.
As far as I can tell, GOG has an internal database that associates the ID of a package with the IDs of the games and DLCs it contains. The tricky part is that GOG can change the association of the bundle with its contents at any time, even changing it retroactively for anyone who owns that bundle.
For example, the only way to buy the game Cyberpunk 2077 at the moment is to go through the package, as you can see from GOGDB: https://www.gogdb.org/products?search=cyberpunk
If one day GOG decides that the package has to contain only "The Adventures of Pinco Pallo" well, you would find in your library the game "The Adventures of Pinco Pallo" and "Cyberpunk 2077" would disappear.
This is what happened when The Elder Scrolls: Arena and The Elder Scrolls II: Daggerfall disappeared, and this is what happened with Spear of Destiny. Someone who for some reason managed to avoid an account refresh can still see the game, but sooner or later it will be forced a refresh and the game will disappear for everyone.
Remember that, again, the only way to buy Wolfenstein 3D is to go through the package. So here's what happened:
On September 15, 2022, GOG renamed the title of package 1441705226 from "Wolfenstein 3D + Spear of Destiny" to "Wolfenstein 3D."
On September 21, 2022, GOG changed the game IDs associated with the package, which were previously the games "1441705046 - Wolfenstein 3D," "1441705126 - Wolfenstein: Spear of Destiny," to "1778420505 - Wolfenstein 3D," and magically the two old games disappeared from our libraries.
Note that the new Wolfenstein 3D is a completely separate game from the old one, it has a new ID, so there is no previous version to go back to with Galaxy.
Now, the last question we don't have an answer to is: Who specifically decided to rename the package and change the associated IDs instead of simply creating a new one? Was it Bethesda that gave the specific order because they wanted to see the old mission packages disappear from existence as if they had never existed? Or perhaps some GOG employee opted for the easy way out by not thinking enough about the consequences of changing an existing package as has happened before?
Given that GOG and Bethesda bounce the responsibilities I don't know if we will ever know.