When you publish custom folders ,they are read-only folders ie these folders cannot be renamed,copied,moved or deleted,though we can create subfolders under these custom folders.
If you remove any of the custom folder from the policy,that custom folder won’t be automatically removed for users,but users would be able to delete that folder.
For example if custom folder "Business Documents" is removed from the policy.The folder will still be visible under Managed Folders,but we do get an option to delete this folder from Outlook.
We can use the –RemoveManagedFolderandPolicy parameter to delete the custom folders.
Set-Mailbox UserA -RemoveManagedFolderandPolicy
above command remove the policy from the user mailbox and delete any custom folders published,including the root Managed Folder’s,provided that these custom folders are empty.
if the custom folders are not empty,the above command converts these custom folders to normal folders,which users can manage.
Note the above command removes all the custom folders ,you cannot selectively choose only one folders to be deleted from user mailbox.
Hope this helps..