Hi,

I sometimes use appt-add as an alarm clock, as it is described in 
(info "(emacs) Appointments"). Recently I started using 
org-agenda-to-appt, and I wanted to update my appointments every 
time that I call the agenda, something like:

#+BEGIN_SRC emacs-lisp
  (add-hook 'org-agenda-finalize-hook (lambda () 
  (org-agenda-to-appt t))) 
#+END_SRC

But this removes the entries that appt-add has added, in other 
words it removes my alarms.

The attached patch permits that, when refreshing, only 
appointments that have the text property org-headline set to t are 
deleted. So it would leave any appointments set by appt-add. I do 
not know if all the entries that org-agenda-to-appt adds have an 
org-headline set to t, from my tests it seems like that is the 
case.

The functionality has backward compatibility (uses C-u C-u), but 
perhaps it would make more sense to use C-u for refreshing only 
org entries and C-u C-u for refreshing everything, or even never 
setting appt-time-msg-list to nil from org.

If the patch is approved to refresh the appointments after every 
agenda buffer is built while keeping those appointments added by 
appt-add, you can do:

#+BEGIN_SRC emacs-lisp
  (add-hook 'org-agenda-finalize-hook (lambda () 
  (org-agenda-to-appt '(16)))) 
#+END_SRC

Best,

--  Jorge.