Custom notifications do not work together with the resend option if you have not set all the email recipients from Notifications to be notified for all submissions.
Email addresses that receive notifications based only on certain conditions, will not be notified when you resend the submission.
If you have email recipient A which receives notifications for all submissions and email recipient B which receives notifications only when the submission contains X, email recipient A will be the only one notified when you resend the respective submission.