Thanks @herf!
Based on that I'd recommend against any of the "defaults write" methods as written above and would edit the posts to warn and say so if they weren't locked.
I get the endorsement of the applescript gui scripting approach.
With that said, it's possible to use them with the addition of using
defaults read $HOME/Library/Preferences/org.herf.Flux.plist disableCount
to get the current number of disabled apps and
defaults write $HOME/Library/Preferences/org.herf.Flux.plist disableCount -integer 0
to set it to zero. You can change 0 to whatever it should be based on the result from the defaults read command. And then combine this with the
defaults write $HOME/Library/Preferences/org.herf.Flux.plist disable-com.google.Chrome false
from my first comment.
It's possible to create better solutions. And this one is apparently more fiddly than I thought it was when I commented my suggestion. My original goal was just to propose a simple solution for the people experiencing an issue w/ f.lux and chrome, but I got sucked in to the challenge(s). Hopefully F.lux for macOS will get an update that can solve them.
And if using the defaults commands messes something up or seem complicated I guess deleting the $HOME/Library/Preferences/org.herf.Flux.plist file, loosing all your current settings in flux and just resetting them is also an option. Editing the file directly with a plist editing tool might also be an easier option, depending.
