If you don't want to show a core, or contrib message to the end user, you now have to iterate $_SESSION['messages'] and search for the (translated, token replaced) string to unset it.

If a message has a unique key, you can easily override a message, or unset it.

function backdrop_set_message($message = NULL, $type = 'status', $repeat = TRUE, $message_key = FALSE) {

A simple unset($_SESSION['messages']['status']['unique_key']) could remove the message, and $_SESSION['messages']['status']['unique_key'] = t('Something else'); changes it.

GitHub Issue #: 
1062