Is there a way to delete all entries within a section? I am currently using FeedMe to import json data every night but I need to delete all entries before doing so to make sure that any orphaned entries are removed.

What is the best way to remove all entries within a section?
I think you're looking for the Delete Duplication Handling option. From the documentation:


  Delete all existing entries in this section, adding only entries from
  this feed. Be careful. Use case: Events, or when only data from the
  current feed is required.
  
  "I want only the entries from this feed in this section."