This only seems to occur with multiple digital object instances. Steps tested:
1. Create resource with component
2. Create 2 digital objects
3. Associate digital objects to component
4. Delete the 1st digital object
5. Delete the 2nd digital object
6. Export EAD (include DAO) – export will still have the 2nd digital object
You can reverse the order of deletes for the same result (1st digital object will remain in EAD export).