As I don't have a Kindle, I could be mistaken, so listen to any Kindle Gurus over my own poor advice.
If I understood you correctly, there are two issues here. One is inconsistent terminology while the other is the overlap between collections. For the inconsistent term, the following should correct the tags within calibre. You will need to change the tag used for all instances
of the wrong term.
- Open the Tag Browser and select the term to be changed/deleted.
- The book list will be limited to all books that the term is associated with.
- Select all.
- Edit Metadata in Bulk.
- Switch to the Search and Replace tab.
- Search for=wrong term
- Replace with=right term
- Click OK.
Once any inappropriate terms are removed, you will need to send the books to the Kindle again in order to get things re-organized.
As to the overlapping collections... I'm not sure how to correct that. Hopefully a guru will come by and offer a suggestion soon.