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In my current setup, I sometimes start emacs with some directories in which I keep my org-mode files, not existing. I.e. for work I use encrypted files, so for example, my ~/projects/foobar/notes doesn't exist, because my ~/projects/foobar directory is empty (because the disk is not mounted into it).

Because of that, when I start emacs and my ~/projects/foobar it not mounted, I get the message:

Non-existent agenda file `~/projects/foobar/notes`. [R]emove from list or [A]bort?

And both options are no good. Abort it obviously not what I want, and Remove removes the directory permamently (by adding org-agenda-files into custom-set-variables section without that directory), so when I later run emacs with disk mounted, the files are not loaded. I need to edit my emacs config, remove that automatically added org-agenda-files in custom-set-variables section, save, exit, restart emacs.

Is there a way to tell org-mode to ignore if the file doesn't exist and just proceed with the files which exists? Ideally, they would be picked up after I refresh agenda, but I can live with being forced to reinitialize my agenda (C-c a a)

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Customize org-agenda-skip-unavailable-files and set it to t.

C-h v org-agenda-skip-unavailable-files says (note that I've customized my setting to t already):

org-agenda-skip-unavailable-files is a variable defined in ‘org.el’.

Its value is t
Original value was nil

Non-nil means to just skip non-reachable files in ‘org-agenda-files’.
A nil value means to remove them, after a query, from the list.

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