Yeah, it's awesome, but I'm talking about the feature where flux automatically starts Yosemite's dark mode after sun set. The problem is that Alfred doesn't change its theme accordingly. I couldn't find something like this in your workflow either, so I created an apple script that switches the Alfred theme. Unfortunately it's not as transparent as a direct API call, but for me at least, it's sufficient.
This script activates themes with the names "OS X Yosemite Auto" and "OS X Yosemite Dark Auto" depending on the dark mode state.
http://pastebin.com/YuH1r5Q8
I tested this Apple Script with the DarkMode workflow and it worked for me.
Next step is to call this script whenever flux starts DarkMode.
Edit:
Wait a second, with "rewrite" do you mean this workflow, right?