I have the F4 GOTY edition from GOG. I have a ton of mods installed like TrueStorms, BodySlide, LooksMenu, LoweredWeapons, Enhanced Lights and FX etc.

I run the game through Vortex (to run with F4SE). Launching through GOG Galaxy always ends up with a crash.

Unfortunately I installed London on the same instance and not over vanilla game. Most of the mods were disabled. The game launches, but only the London “DLC” can be played. I disabled the London-related modules in Vortex and more or less restored the pre-installation state. However, loading my saves from the “normal” game I still have, for example, “portable radio” instead of Pipboy :D.

Is it possible to uninstall London and clear the modified game instance?

What is the best way to do to have two instances of the game: GOTY + mods and vanilla + London.

In short, I don't think there is a way to have two instances.

The challenge is that Fallout 4 / Fallout London both need your \My Documents\My Games\Fallout4, and any information in there (saves, preferences, changes to the ini files) directly affects any FO4 game that uses it.

Unfortunately FO4 cannot be changed to look at a different folder, and I do not believe a mod can change that save location, since it is part of the games' core.

What you could do however is backup said folder after every time you play, then delete and replace the files in there with the backup from the other game - a bit tedious, but could potentially be a workaround if you absolutely want to have both games available to you.

Look at my post:

https://www.gog.com/forum/fallout_london/fallout_london_remember_about_the_right_way_to_launch_it

Mind The Gap!