I don't know for sure but what I have deduced from my own bit of reading on the subject is that they both involve adrenal issues, yes, CF is usually accompanied or kicked off with flu like symptoms. Many people with AF also have the Epstein Barr virus, i think there must be some connection there and that the flu like symptoms of CF could be that.
But i don't think one can really have one issue and get the other or that one is necessarily worse than the other. I think they may be closely related if not the same thing being put under different labels by different drs.
Pain and inflammation can be a symptoms of AF and i get sore throats all the time when I am overloaded with toxins.