There’s a thing or two to be said about the sense and nonsense of antivirus Apps on smartphones, but in the end that doesn’t matter here, because the amount of stuff they can prevent from happening is just a small subset of what could happen to an OS installation.
OSes are much too complex for vendors to foresee or test every possibility of how automatic procedures like upgrades or possible interactions with any App might turn out.
Or you could say the software industry as a whole is still missing tools or regulations to properly manage the levels of complexity it generates itself.
Anyway … if you are not suffering from a hardware defect and you want to have a working phone, then wiping the phone completely, formatting the data partition, and then installing from scratch whatever OS and OS version you want will restore the phone to a working state.
That’s what a factory reset should do, but in our case doesn’t. And the wiping which a manual installation of Fairphone OS or Fairphone Open OS does by itself will delete all files, but might leave the directory structure intact.
Usually the pseudo factory resets and the manual installation procedures work out like intended somehow nonetheless, but if not … really installing from scratch is the choice left.
If you are not feeling confident about it, which I can understand because it all seems drastic, perhaps #fairphoneangels could assist, if you happen to have any in the vicinity.
Links to the manual installation files for Android 6 are given in the downgrade section of the post mentioned before.