I can think of three methods (in the following, for definiteness, I assume you use the recursive method to construct org-agenda-files in your init file; the changes required for the list method should be obvious). In increasing order of complexity:
Interactively add every new agenda file
If you create a new file, add content and at some point you decide that ...
Per NickD's comment this may well be a bug. In the meantime, it looks like this does what you're aiming for (or at least points you in the right direction):
(defun dunne//add-deadline-warning (w)
(let* ((regexp org-deadline-time-regexp))
(if (not (re-search-forward regexp (line-end-position 2) t))