We noticed that Brother scanners worked properly with Paperless with High Sierra and previous operating systems however once Mojave came out, Paperless didn't appear to be "seen" when trying to scan. We have contacted both Brother and Apple who have confirmed there is an issue in Mojave. Brother, in fact, has sent us this statement.
"Brother does not support scanning with 3rd party apps, while they may work with Twain drivers or apple drivers directly to the app, we don't have any specific support for those programs."
So, unfortunately at this time and until Apple or Brother can update their code, Brother scanners working with a Mac running Mojave, aren't compatible with Paperless.