Turning off completed download handling will stop Sonarr from trying to import files, with a proper download client Sonarr will still track the downloads, but stop tracking once it's complete, with blackhole disabling may not actually solve anything come to think of it, since it'll still try to track things which is the whole problem.
Have you pointed the
Watch Folder at your sorted media files? If so, you'd want to point it at another unrelated folder, since you're using something else to import you don't want Sonarr to try. If not, what folder have you pointed it at?
Since something else is importing the files, you'll either want to have that tell Sonarr to rescan the series folder (using the API: https://github.com/Sonarr/Sonarr/wiki/Command#rescanseries) or Sonarr will only see the updates when it updates every 12 hours during the series refresh.