App Engine returning inconsistent results

I am having some confusion with a long-time app engine in my PS Campus Solutions environment. I have a SQL object in an app package, which is part of an app engine that produces a .csv file of faculty/employees for logon data, then transferred to a third party. This SQL object pulls a list of people from 2 tables, and when I query with that object's SQL in our databases (prod and dev), it returns exactly as I need. The file was 61KB after being created and written to, which I noted. After a while, I was notified some people