I was fiddling with my init file and something with pdf-tools blew up and 
initialization went wrong and I lost my desktop history list of buffers I always 
have open.  When I fixed the problem (by dropping pdf-tools, which I realized I 
never used), I had to load all the files I like to have open.  I opened four, 
and for each one I got the same warning, as you can see below.  Further below 
that is the full Org debug dump.

I don't know if the ivy-done clue is enough to be helpful (maybe it just means 
there's something funny involving ivy), but if there's more I can do I'm glad to 
help.

Bill


Warning (org-element-cache): org-element--cache: Unregistered buffer modifications detected. Resetting.
If this warning appears regularly, please report the warning text to Org mode mailing list (M-x org-submit-bug-report).
The buffer is: reading-diary.org
  Current command: (ivy-done 7688 7689)
  Chars modified: 7688
  Buffer modified: 7689
  Backtrace:
nil Disable showing Disable logging
Warning (org-element-cache): org-element--cache: Unregistered buffer modifications detected. Resetting.
If this warning appears regularly, please report the warning text to Org mode mailing list (M-x org-submit-bug-report).
The buffer is: pepys-exchange-list.org
  Current command: (ivy-done 5351 5352)
  Chars modified: 5351
  Buffer modified: 5352
  Backtrace:
nil Disable showing Disable logging
Warning (org-element-cache): org-element--cache: Unregistered buffer modifications detected. Resetting.
If this warning appears regularly, please report the warning text to Org mode mailing list (M-x org-submit-bug-report).
The buffer is: l2a.org
  Current command: (ivy-done 26 27)
  Chars modified: 26
  Buffer modified: 27
  Backtrace:
nil Disable showing Disable logging
Warning (org-element-cache): org-element--cache: Unregistered buffer modifications detected. Resetting.
If this warning appears regularly, please report the warning text to Org mode mailing list (M-x org-submit-bug-report).
The buffer is: library.org
  Current command: (ivy-done 779 780)
  Chars modified: 779
  Buffer modified: 780
  Backtrace:
nil Disable showing Disable logging







Emacs  : GNU Emacs 29.0.50 (build 5, x86_64-pc-linux-gnu, GTK+ Version 3.24.20, 
cairo version 1.16.0)
  of 2022-05-07
Package: Org mode version 9.5.3 (release_9.5.3-473-g15d256 @ 
/usr/local/src/org-mode/lisp/)

current state:
==============
(setq
  org-link-elisp-confirm-function 'yes-or-no-p
  org-ditaa-jar-path "/usr/share/ditaa/ditaa.jar"
  org-hide-emphasis-markers t
  org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3 "\n\n(fn 
ENTRY)"]
  org-babel-after-execute-hook '(org-redisplay-inline-images)
  org-persist-after-read-hook '(org-element--cache-persist-after-read)
  org-export-before-parsing-hook '(org-attach-expand-links)
  org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe 
org-babel-header-arg-expand)
  org-archive-hook '(org-attach-archive-delete-maybe)
  org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines 
org-cycle-optimize-window-after-visibility-change)
  org-persist-before-read-hook '(org-element--cache-persist-before-read)
  org-image-actual-width nil
  org-mode-hook '((lambda nil
 		  (org-superstar-mode 1))
 		 wtd/org-ispell
 		 add-org-toggle-src-key
 		 org-appear-mode
 		 turn-on-flyspell
 		 (lambda nil
 		  (setq
 		   prettify-symbols-alist
 		   (cons '("<=" . 8804)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons '(">=" . 8805)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons '("|>" . 9655)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons
 		    '("#+BEGIN_SRC" . 9121)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons
 		    '("#+END_SRC" . 9123)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons
 		    '("#+begin_src" . 9121)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons
 		    '("#+end_src" . 9123)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons
 		    '("#+BEGIN_QUOTE" .
 		      10077)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons
 		    '("#+END_QUOTE" . 10078)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons
 		    '("#+begin_quote" .
 		      10077)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons
 		    '("#+end_quote" . 10078)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons '("[ ]" . 9744)
 		    prettify-symbols-alist)
 		   )
 		  (setq
 		   prettify-symbols-alist
 		   (cons '("[X]" . 9746)
 		    prettify-symbols-alist)
 		   )
 		  )
 		 add-org-close-all-drawers-key
 		 (lambda

 						nil

 						(setq ispell-parser 'tex)

 						)
 		 (lambda nil
 		  (org-toggle-inline-images))
 		 org-clock-load
 		 #[0
 		   "\300\301\302\303\304$\207"
 		   [add-hook
 		    change-major-mode-hook
 		    org-fold-show-all append
 		    local]
 		   5]
 		 #[0
 		   "\300\301\302\303\304$\207"
 		   [add-hook
 		    change-major-mode-hook
 		    org-babel-show-result-all append local]
 		   5]
 		 org-babel-result-hide-spec
 		 org-babel-hide-all-hashes
 		 #[0 "\301\211\207"
 		   [imenu-create-index-function org-imenu-get-tree]
 		   2]
 		 wrap-region-mode)
  org-babel-load-languages '((ditaa . t)
 			    (dot . t)
 			    (latex . t)
 			    (lilypond . t)
 			    (python . t)
 			    (R . t)
 			    (ruby . t)
 			    (shell . t)
 			    (sql . t)
 			    (sqlite . t))
  org-src-window-setup 'current-window
  org-fold-core-first-unfold-functions '(org-fold--hide-drawers 
org-fold-hide-archived-subtrees)
  org-ellipsis " ⬎"
  org-confirm-shell-link-function 'yes-or-no-p
  outline-isearch-open-invisible-function 'outline-isearch-open-invisible
  org-startup-indented t
  org-highlight-latex-and-related '(latex)
  org-use-speed-commands t
  org-agenda-before-write-hook '(org-agenda-add-entry-text)
  org-src-preserve-indentation t
  org-babel-tangle-lang-exts '(("ruby" . "rb")
 			      ("python" .
 			       "py")
 			      ("LilyPond" .
 			       "ly")
 			      ("latex" .
 			       "tex")
 			      ("emacs-lisp"
 			       . "el")
 			      ("elisp" .
 			       "el")
 			      )
  org-src-mode-hook '(org-src-babel-configure-edit-buffer 
org-src-mode-configure-edit-buffer)
  org-confirm-elisp-link-function 'yes-or-no-p
  org-cycle-separator-lines 0
  org-superstar-headline-bullets-list '("⊢"
 				       "ǁ"
 				       "ǀ"
 				       "⋱"
 				       "◉"
 				       "○")
  org-support-shift-select t
  org-pretty-entities t
  org-fontify-whole-heading-line t
  org-speed-command-hook '(org-speed-command-activate 
org-babel-speed-command-activate)
  org-export-backends '(html latex md odt
 		       beamer)
  org-confirm-babel-evaluate nil
  org-fold-core-isearch-open-function 'org-fold-core--isearch-reveal
  org-clock-persist 'history
  org-persist-before-write-hook '(org-element--cache-persist-before-write)
  org-tab-first-hook '(org-babel-hide-result-toggle-maybe 
org-babel-header-arg-expand)
  org-link-shell-confirm-function 'yes-or-no-p
  org-babel-pre-tangle-hook '(save-buffer)
  org-agenda-loop-over-headlines-in-active-region nil
  org-occur-hook '(org-first-headline-recenter)
  org-metadown-hook '(org-babel-pop-to-session-maybe)
  org-link-parameters '(("attachment" :follow
 			org-attach-follow
 			:complete
 			org-attach-complete-link)
 		       ("eww" :follow
 			org-eww-open :store
 			org-eww-store-link)
 		       ("rmail" :follow
 			org-rmail-open
 			:store
 			org-rmail-store-link)
 		       ("mhe" :follow
 			org-mhe-open :store
 			org-mhe-store-link)
 		       ("irc" :follow
 			org-irc-visit :store
 			org-irc-store-link
 			:export
 			org-irc-export)
 		       ("info" :follow
 			org-info-open
 			:export
 			org-info-export
 			:store
 			org-info-store-link)
 		       ("gnus" :follow
 			org-gnus-open :store
 			org-gnus-store-link)
 		       ("docview" :follow
 			org-docview-open
 			:export
 			org-docview-export
 			:store
 			org-docview-store-link)
 		       ("bibtex" :follow
 			org-bibtex-open
 			:store
 			org-bibtex-store-link)
 		       ("bbdb" :follow
 			org-bbdb-open
 			:export
 			org-bbdb-export
 			:complete
 			org-bbdb-complete-link :store org-bbdb-store-link)
 		       ("w3m" :store
 			org-w3m-store-link)
 		       ("doi" :follow
 			org-link-doi-open
 			:export
 			org-link-doi-export)
 		       ("id" :follow
 			org-id-open)
 		       ("file+sys")
 		       ("file+emacs")
 		       ("shell" :follow
 			org-link--open-shell)
 		       ("news" :follow
 			#[514
 			  "\301\300\302Q\"\207"
 			  ["news" browse-url
 			   ":"]
 			  6
 			  "\n\n(fn URL ARG)"]
 			)
 		       ("mailto" :follow
 			#[514
 			  "\301\300\302Q\"\207"
 			  ["mailto"
 			   browse-url ":"]
 			  6
 			  "\n\n(fn URL ARG)"]
 			)
 		       ("https" :follow
 			#[514
 			  "\301\300\302Q\"\207"
 			  ["https"
 			   browse-url ":"]
 			  6
 			  "\n\n(fn URL ARG)"]
 			)
 		       ("http" :follow
 			#[514
 			  "\301\300\302Q\"\207"
 			  ["http" browse-url
 			   ":"]
 			  6
 			  "\n\n(fn URL ARG)"]
 			)
 		       ("ftp" :follow
 			#[514
 			  "\301\300\302Q\"\207"
 			  ["ftp" browse-url
 			   ":"]
 			  6
 			  "\n\n(fn URL ARG)"]
 			)
 		       ("help" :follow
 			org-link--open-help
 			:store
 			org-link--store-help)
 		       ("file" :complete
 			org-link-complete-file)
 		       ("elisp" :follow
 			org-link--open-elisp)
 		       )
  org-metaup-hook '(org-babel-load-in-session-maybe)
  org-startup-with-inline-images t
  org-return-follows-link t
  org-special-ctrl-a/e t
  org-tags-column 120
  org-hide-macro-markers t
  org-footnote-section nil
  org-list-allow-alphabetical t
  )
-- 



--
William Denton
https://www.miskatonic.org/
Librarian, artist and licensed private investigator.
Toronto, Canada