That's the weirdest thing, having the same game published by two companies on two different platforms, how can two companies hold the rights to the same game? copyrights is teh hard
Often it is because one company publishes the game before another company gains the publishing rights. The original contract with the first company remains in force until it expires in which case the second company can decide to continue publishing under a new contract.
A transfer in rights doesn't usually negate previous contracts - although it could depending on the wording of the original contract if it stipulates as such specifically.
The IP rights to The 7th Guest are owned by Trilobyte LLC. Trilobyte LLC probably worked with GOG on the first re-release of The 7th Guest via DOSBox or SCUMMVM. However, they later partnered with Nightdive Studios for their "25th Anniversary" release on Android. The 25th Anniversary edition included a variety of extras like a copy of the 7th Guest novel and a bunch of other things.
I don't know if that carries over into the Steam version by NightDive or not.
But that is how 2 publishers can publish the same game. Technically the original game was published by Trilobyte Inc back in the early 90s. However, that company went bankrupt, largely due to management and game production style differences between the original co-founders. The IP Rights to The 7th Guest franchise seemed to be up in the air for a while but, reverted to or were purchased by Rob Landeros who formed Trilobyte LLC to deal with The 7th Guest and other IPs he held on to.
As to why Trilobyte decided to pull the GOG version, anything we say is speculation. It could have to do with the NIghtDive vs. the original Trilobyte LLC restoration. I don't think there are currently any plans for a true HD remake because Trilobyte doesn't have the original bluescreen footage of the actors. It's impossible to re-scale the game without having access to that original footage, period.
I've personally been trying to track down the original SVHS or Beta tape(s) from the game by talking to former producers and developers. This is mostly because I love seeing behind the scenes stuff and outtakes. It's been an interesting journey getting to speak with people who developed games in the "wild west" days of CD-Rom development. That being said, none of them, including the original videographer or people who did the masking work have a copy as of right now.
So again my best guess is similar to what others said. Trilobyte LLC had a version but, they also partnered with NightDive for a version. Trilobyte likely wants to make things as easy to manage as possible and probably decided they don't want to manage 2 versions of the same game. Hopefully this means the NightDive version will show up on GOG in the future.
As for The 11th Hour, well, that source code has long been missing and any fixes to it are completely reverse engineered. That is another "lost" asset that disappeared when Trilobyte LLC dissolved.
Note: I don't work for Trilobyte. I am involved with The 13th Doll, which is a fan game based in the 7th Guest universe.
Trlobyte likely had zero expertise in programming/porting, so they went to GOG/Nightdive to do the heavy lifting. Its likely less about 'having an in' but more 'we dont want to port this here is some money'
Given the game is still on steam it seems like the likely situation might be:
1) GOG goes to Trilobyte for 7th Guest release
2) GOG works on the release, release it Feb 9 2012
3) Next year Trilobyte wants to release on steam
4) Realizes GOG basically wont let them release GOG code on steam
5) gets Nightdive studios to do the work
6) Gets game on steam Oct 18, 2013
7) Nightdive realizes they're losing revenue on the GOG version
8) remove game on GOG in preparation for moving the publishing back end to NightDive instead of Trilobyte
Kind of a guess but given that happened with the Fallout series when it was removed then put back in when rights transfered to Bethesda. Since its only happening on one platform rather than both simultaneously, that's my best guess given the limted information
Problem with #4, in the NoClip GOG documentary they said that they always allow the IP holder to re-sell the updated/fixed versions elsewhere if they want to.
However, I think you might be correct about the NightDive thing.