Users will only be counted once in both funnel and journey analysis. If a user reaches a fork in a journey, they will be counted in whichever path they do first. If you create an identical funnel and journey, you may find that users are doing a different step in the journey before they make it back to the path you originally created.
For examples of how to look at alternate paths in a Journey chart, see the Use cases & examples section of the Journeys overview guide.