I have been having issues with recentf for quite a while: even I close emacs gracefully very oftern used files would not be in recent files next time.
My recentf config looks like
(use-package recentf
  :config
  (setq
    recentf-save-file "~/.cache/emacs/recentf"
    recentf-max-saved-items 10000
    recentf-max-menu-items 5000
    )
  (recentf-mode 1)
  (run-at-time nil (* 5 60) 'recentf-save-list)
  )
Recently I have noticed this
Saving file /home/yuki/.cache/emacs/recentf...
Wrote /home/yuki/.cache/emacs/recentf
Saving file /home/yuki/.cache/emacs/recentf...
Wrote /home/yuki/.cache/emacs/recentf
Error: (file-missing "Doing chmod" "No such file or directory" "/home/yuki/.cache/emacs/recentf")
Saving file /home/yuki/.cache/emacs/recentf...
Wrote /home/yuki/.cache/emacs/recentf
Saving file /home/yuki/.cache/emacs/recentf...
Seems like at some point file disappears or something. Did anyone have similar problems? Any ideas what can go wrong (may be multiple instances)?
                        
I suspect something is loading
recentfearlier than you expect (for me it was triggered by arequireinconsult.el, which mean that it loads the recentf list from the wrong place because you haven't yet set it to your location. Later, when the(run-at-time ...)fires, you store only those files that have been loaded since startup and the cycle continues...TL;DR - You need to move your setup from
:configto:init.