We have an on premise install of SharePoint 2013. Using our farm account, let's say spfarm, we built out a handful of web applications. Since it is the farm account, it inherently gets full access to all site collections created under it by default. Somehow, on one of our web applications, the spfarm account has had it's permissions revoked. Does anyone know how the farm account could mysteriously have all of it's default inherited permissions removed and it no longer has access to the site?
More Information: The farm account still has DBO access to the content database for the problematic web application. Also, in an attempt to fix the issue, we deleted the web application, but kept the content DB in tact. Then re-created the web application and attached it to the existing content DB. The problem was fixed briefly, but then coming in to work the next day, the exact same problem came back and the farm account lost all permissions again. Seems to point to a timer job or some process killing it off. We don't have any custom scheduled jobs either.