Blackberry has not given a final fix for this but the link has some options to try.
They state this problem is seen when deleting multiple emails at one time.
Another bug in a long line of bugs.
the link
KB35669-When deleting messages from the BlackBerry Hub, messages are deleted from both the BlackBerry Hub and the mail server even though the "Delete On" setting is set to "Handheld Only" or "Prompt"