Hey, I know this topic is a bit old, however I ran into the same issue today and I would like to share this fix I found for anyone who follows.
To block f.lux from keeping the PC awake, but still allow it to control your Hue lights when the PC is on, open a command prompt window in administrator mode by opening the search bar (Windows 10), searching for "command" and right clicking the command prompt and selecting "Run as administrator". Next, in the command window, type these two commands (confirm each by pressing enter):
powercfg /requestsoverride PROCESS flux.exe SYSTEM
powercfg /requestsoverride PROCESS flux.exe AWAYMODE
After that, f.lux should no longer prevent your PC from entering sleep mode.
Hope this helps!