org-projectile is a small Emacs package that makes it easy to associate org-mode TODO items with projectile projects.

Each projectile project can have its own, but sometimes projects don’t have one (or don’t need one) and these empty files are still added to the agenda.

The following function filters the org-projectile list of TODO files and removes any file that doesn’t actually exist.

(defun sodaware/org-projectile-todo-files () 
  "Fetch a list of org TODO files for projects that actually exist."
  (seq-filter #'file-exists-p (org-projectile-todo-files)))

;; Add org-projectile files to org.
(setq org-agenda-files (append org-agenda-files (sodaware/org-projectile-todo-files)))