Better Touch tool is definitely the way to go. When you create a new shortcut, in the actions there is a whole category called "Navigating Spaces / Desktops". Within it you can then pick an action such as 'move left a space', 'switch to desktop 3', etc. Check it out and let us know!
Go to the 'Display' tab and check the 'Scaled' option instead of 'Default for display' (or vice-versa). Then, simply select whichever text option fits you better.
Once you select one, the display will reset automatically and you'll be having the correct display profile along with Night Shift working again.
Added the solution to Apple forums as well.
1) In a Finder window Go to Applications.
2) Locate the application's icon and do a Get Info.
3) In the top left corner of the Get Info window the correct non-generic application icon should be displayed.
4) Select that icon using the mouse.
5) Do an Edit->Copy on the icon in the top left corner of the window.
6) Do an Edit->Paste on the icon in ...