For what it's worth, when this happens, I generally pkill -SIGUSR2
emacs. emacs reacts to the USR2 signal by stopping everything and start
a lisp debugging session. From there, I reset all the org caches with
this command:

--8<---------------cut here---------------start------------->8---
(defun konix/org-element-cache-reset-all ()
  (interactive)
  (mapc
   (lambda (file)
	 (save-window-excursion
	   (save-excursion
		 (find-file file)
		 (org-element-cache-reset)
		 )
	   )
	 )
   (org-agenda-files)
   )
  )
--8<---------------cut here---------------end--------------->8---

Finally, I quit the debugging session and reset the debug on quit with
(toggle-debug-on-quit) and everything comes back to normal.

My two cents,
-- 
Konubinix
GPG Key    : 7439106A
Fingerprint: 5993 BE7A DA65 E2D9 06CE  5C36 75D2 3CED 7439 106A