The new documentation of the episode service https://opencast.jira.com/wiki/display/MH/The+EpisodeService
does state this: "It is important to note that it is necessary to place the archive operation after the encoding but before the publishing operation, since publishing modifies the media package."
Unfortunately the archive operation in compose-distribute-publish.xml in all current Matterhorn versions is the just before the clean-up operation at the end of the workflow definition.
In our 1.4.4 production environment we encountered problems with files missing in the archive because that could be fixed by moving the archive operation before the publish operations. And we are very thankful for the documentation to finally find the reason for this.