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.
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