I am playing offline and notice several things.
First, when I play online, my CoF faction is shared between every character that I create. Offline, I have to restart at 0 with each one after unlocking it.
Second, every day, I grind to faction rank 4 on one character, log out and back in the next day and it is reset to rank 1.
This is truly becoming annoying.
I wanted to bump this as I’m suffering through something similar. My faction reputation seemed to be climbing steadily between game sessions, but I’ve now logged into this character and all my reputation and favor gained is gone completely!
I exclusively play offline, so I’m not sure if it’s related to Mouadieb’s similar issue or not.
Steam Cloud bug… if you play offline you can off it 
I have Steam Cloud disabled by default.
Besides, it couldn’t have been that. My level progress, my lens, and the prophecies I purchased just before I logged off my character are still there. It’s just that the favor and reputation were completely wiped, and I have no idea how I can replicate that for anyone to fix.
Same. I just started playing online so I do not have to keep grinding more faction each time I log in just to replace what was lost by logging out.
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