I just reinstalled both versions and this does seem to be the case. The smaller one (12MB) is just Wolf3D without the expansion. The larger one (18MB) is Wolf3D + Spear, but without the mission packs. The game and expansion are installed to the same folder and there's a launcher which allows you to select which you want to play. I didn't do a checksum between them, but at least the file sizes between the two sets of wolf3d.exe and *.wl6 files are the same - so it doesn't appear that the Bethesda release changed anything in the game itself.

The standalone Spear of Destiny installer does include both mission packs, as before. It installs to a separate folder and does not require Wolf3D to be installed. Just for kicks, I tried copying the "M2" and "M3" mission pack folders into the Bethesda Wolf3D + Spear version. The new combined launcher does not recognize the mission packs (it looks to be a hard coded .exe file with no way to add entries to it).

I also noticed the game page (https://www.gog.com/en/game/wolfenstein_3d) does not mention the mission packs. So I'm not sure whether someone who buys the game now will still get them. I seem to remember they were made by a third-party, so Bethesda may not be able to distribute them due to the original contract terms.

Issue come from using packages for all Bethesda games (originally that was for Elder Scrolls 1\2 free versions bundled with all releases here, but early in 22 they been unbundled from packs and released for everyone separate).

That obviously sup[posed to be separate product for old and new owners - that's why there is new appid. But they forgot to make new pack. Or to be more correct, since it is new ID it is GOG(+Bethesda) who bring this update from Bethesda, not just update (which ones time to time made without GOG, by automatic publishing scripts in GOG Galaxy API). And GOG too lazy to make new pack - cause it need make new store page. Laziest GOG staff person use older one just as is.

So that lead everyone got same product - same package. With both old APP ID games removed, and all got new app id game.
Fixing that require more job than make it properly in the first place. Im surprised that they fix that. They do fix it, right? Even if they just re-add manually everyone SoD as separate product (and Wolf3D now 18 mb installer version with launcher), just like in Steam...
Or they even made that prev owners get all 3 Wolf3D app id products? Unlike GOG, Steam version is exactly an update for original appid game and they get 1,5 SoD, so they have two games. What for GOG - it is now two or three?

I just saw that Spear of Destiny appeared in my library again, thanks for everyone who nagged GOG about fixing this. Great job guys!

Sorry to necro this thread. Has any solution been found for this? Some have said that it reappeared in their library and unfortunately, it has not reappeared for me. I luckily have the original downloaded and noticed it gone from my library.

Same here. Just noticed it's gone form my library as well.
I had both Wolf 3D and Spear of Destiny installed the whole time, but now GOG Galaxy won't recognize them as installed and instead I have just one Wolfenstein 3D game in my library that says it's not installed.

Super annoying isn't it? I'm currently unsure of GOG's customer support response times but I have an open ticket regarding this, so far it's been just under two weeks and heard nothing. I shall let you know if I hear anything back from them.

gee, thanks gog, due to your stupid fucking robot i have to come to this wretched forum to fix an issue.
i'm having the same problem. spear of destiny is missing from my account. the main spear of destiny expansion is now bundled with normal wolfenstein 3d, but not the mission packs.
"but they're not good-" i don't care. i paid for a thing and it has- intentionally or not- been taken from me. that is the problem here.

Yeah, I did the same and now have SOD with all the content separate again. Worked perferctly. Thanks.

Another recommendation: Make multiple copies of your Wolf 3D and all the Spear of Destiny offline installers.

Put them on as much external storage that you have.

I read the full post - checked and I have both games as single purchases and SOD has RD & UC.

Interestingly, when I look at Wolf 3D or SOD in my library, the more does not show a store page (expected). But when I look up Wolf 3D in the store, it says I already own it. UPDATE - I looked and I have *2* entries for Wolfenstein 3D - one with a store page link and the other with a changelog link. The one with the store link has an 18MB download and the one that is not in the stores has the 12MB download. interesting...so they gave me the new combined one and I have the two older separated ones as well...

I wish they would fix that with some of the other bundles. I bought a big bundle of Wolfenstein II New Colossus that included both English and German versions of New Colossus as well as both English and German versions of The Freedom Chronicles (episodes 0, 1, 2, and 3), but they keep showing me sale prices for NC deluxe and Freedom Chronicles - and make it look like they are NOT in my library, when they actually are... Are the German versions available any more? Both English and German versions have a store page link that just goes to the standard edition of the English version... maybe the German version was a short time special?

Just as info for people who never realised that original SOD and Wolf3D was merged and are now late in writing to support to get the split entry back... it seems like support is now not helpful anymore. I even linkend them this thread in my request and this is what I got as answer:

"Hello,

Due to the publishers suggestion, Wolfenstein and Wolfenstein: Spear of Destiny have been merged into one release.
Please could you get in touch directly with the publishers of the game to clarify this further?
https://help.bethesda.net/#en/home

Best regards,
xxx
GOG Customer Support