Hello Ewen Wilson,
Thank you for reaching out to Apple Support Communities, and we'll be happy to help in any way we can. We understand you're having issues with deleting folders in Mail on your Mac. To start, follow the steps listed here to see if they resolve the issue: Create or delete mailboxes in Mail on Mac - Apple Support
"Delete mailboxes
WARNING: Deleting a mailbox permanently deletes the mailbox and its contents (including other mailboxes), and can’t be undone.
- In the Mail app
on your Mac, select a mailbox in the Mail sidebar. - Choose Mailbox > Delete Mailbox.
- If you have problems deleting a mailbox on the server for an IMAP account, contact the provider of your account.
When you delete a Smart Mailbox, the messages it displayed remain in their original locations.
If you use the Finder to delete a mailbox, the change may not appear in Mail.
Note: If you set up Time Machine to back up files on your Mac, you can use the backups to restore content that Mail downloaded (based on options set in Mail and on your Mac). See Restore items backed up with Time Machine."
We hope this helps.
Cheers!