GoldenChaos has been stuck at Applying settings, please wait... since last 2 hours. This happened after I updated BTT to the latest version. I also tried moving to the Alpha version but the same issue persists.
Also, do I lose all my settings of GoldenChaos when I update the BTT?
Open the GoldenChaos-BTT settings window (Command + Option + Shift + P) and click “Check Settings”, it should refresh the GC Touch Bar display and get rid of that message 
And nope, you don’t lose any of your GC settings when upgrading BTT or GC!
Before I got your reply, I was trying to fix the issue and, in irritation, deleted the Golden Chaos preset and reinstalled it. What I loved here is even after deleting and reinstalling GC, all my settings were added again. Wow! Only a few custom settings I had done on BTT were not added. They are easy to add. Also, in trying to fix it, learnt about the two-finger scroll to change the volume. Thank you, @GoldenChaos. Appreciate your UI and coding skills. 
Hi,
"Check Settings" Used to fix it for me but doesn't anymore. I have completely reset my mac and since then permanently have that "apply settings, Please wait". Just where Spotify commands should be. Rest works fine but I definitely can't fix that one. Anyone would have an idea? Many thanks!
Were you able to solve this? I am having the same issue. Had a fresh install over the weekend and it's stuck on applying settings since. And the "Check Settings" button does not help in my case either.
No I couldn't. No idea how to fix this sorry.
I'm checking what's wrong, should have more details tomorrow.
To get rid of the "Applying Settings" you can execute this apple script:
tell application "BetterTouchTool"
update_trigger "F64CCCA5-39D9-46D0-A2D8-092515FFE83B" json "{\"BTTEnabled2\" : 0}"
end tell
E.g. via Apple's Script Editor app. However I'm not yet sure what's the underlying problem that causes this to happen.
I think the issue should be resolved with BTT 4.392 alpha (uploading now).
You'll need to delete & reimport the preset.