I am having the exact same issue on a Huawei Honor Note 8 running EMUI 4.1 (Android 6.0). With f.lux on, I will get random reboots 1-3 times a day. With f.lux disabled in Titanium Backup, my phone doesn't reboot randomly.
I understand that f.lux is a preview version and not a final product. I really like the features of it so far, like the mentioned tuning for AMOLED and all of the automated switching.