I had the same issue, with cpanel I was able to resolve it by going into the mail directory and editing the file:
/mail/yourwebsite/yourusername/courierimapsubscribed
Which should look something like this:
INBOX
INBOX.Drafts
INBOX.Sent
INBOX.Junk
INBOX.Trash
INBOX.Registrations
INBOX.Family
INBOX.Friends
I also deleted a file by the same name of the folder that I was removing, I think it was in one of the folders in the same directory, but I forget which... maybe someone who is more familiar with the IMAP structure could tell you (as well as explain what might have happened with roundcube that it lost the ability to delete it)
keywords:
Can't Delete Folder ; Folder won't delete ; folder doesn't work