I had used the email user feature to email around 49K users. Since then random normal notification mails are delayed by around 6 hours. Is there a way to check and clear the backlog to prevent the normal mails from getting delayed?
The backlog is likely in your MTA itself, such as postfix, as XF doesn't currently do mail queuing. I assume you have root access to the server, as otherwise you won't be able to do anything, but what you would have to do is specific to your MTA.