The docstring for org-agenda-skip-unavailable-files says: 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.
However, doing a grep over the org mode code, the only place where this variable is checked is in org-agenda-files (it is also let bound in exactly two places): (when org-agenda-skip-unavailable-files (setq files (delq nil (mapcar (function (lambda (file) (and (file-readable-p file) file))) files)))) The behavior appears to be contrary to the docstring: A non-nil value means silently remove non-reachable files and a nil value means do nothing. Or so it appears. Actually, the querying for removal happens in org-check-agenda-file. It looks like the "just skip non-reachable files" is implemented by filtering them out so we don't call org-check-agenda-file on them later. The problem is that when org-agenda-file-to-front or org-remove-file is called, any non-reachable files get filtered out from org-agenda-files and then saved back to the user's customizations. The result is that setting org-agenda-skip-unavailable-files to t ends up remove the user's un-reachable agenda files rather than skipping them, contrary to the docstring. If a user did not realize this, they may end up missing important items on their agenda, if they have some agenda files that are sometimes missing and get removed from org-agenda-files (e.g., mounted via a network drive), so in my opinion this is a serious bug. Emacs : GNU Emacs 26.3 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.10) of 2019-08-29 Package: Org mode version 9.2.6 (9.2.6-5-g9c611f-elpaplus @ /home/ionasal/.emacs.d/elpa/org-plus-contrib-20191111/)