Hello Daniel O'Neil,
This question was answered in the ticket that you submitted, but I also wanted to add my response here for other users.
We currently do not have the functionality to role any Navigation changes back, other than doing it manually.
What I would recommend would be to test out these changes in the Preview Environment (https://customercare.igloosoftware.com/support/knowledgebase/all_articles/articles/digital_workplace_preview) first. Then you can verify that the changes that were made were successful, and then apply the same changes to the live Production site.