[BUG] subheadings disappear from buffer [9.6.6 (release_9.6.6 @ /opt/local/share/emacs/29.1/lisp/org/)]

[Peter Mao <peter.mao@gmail.com>]

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This is an incomplete initial bug report.  I don't have time right now to
chase down all the details.

A couple of times in the past month, the subheadings in the org file I'm
working on (with lots of org-babel code blocks) disappear.  <TAB> does not
fold or unfold those headings, although the indicator (...) still shows.
In desperation, I switch to fundamental-mode, but the text is still not in
the buffer.  I save the buffer under a different filename to find that all
the missing text is in the file.

Has anyone else seen this?

summary:
1. subheading text disappears from org file, even in fundamental
2. saving the buffer shows that the disappearance is cosmetic only
3. I have not established reproducible conditions for this yet.


Emacs  : GNU Emacs 29.1 (build 2, x86_64-apple-darwin22.5.0, GTK+ Version
3.24.38, cairo version 1.17.6)
 of 2023-08-07
Package: Org mode version 9.6.6 (release_9.6.6 @
/opt/local/share/emacs/29.1/lisp/org/)

current state:
==============
(setq
 org-noter--doc-goto-location-hook '(org-noter-pdf--goto-location)
 org-link-elisp-confirm-function 'yes-or-no-p
 org-ditaa-jar-path "/opt/local/share/java/ditaa-0.11.0-standalone.jar"
 org-noter-supported-modes '(doc-view-mode pdf-view-mode nov-mode)
 org-bibtex-headline-format-function #[257 "\300 \236A\207" [:title] 3
"\n\n(fn ENTRY)"]
 org-download-file-format-function 'org-download-file-format-default
 org-agenda-files '("~/Syncbox/files/gtd.org")
 org-persist-after-read-hook '(org-element--cache-persist-after-read)
 org-export-before-parsing-hook '(org-attach-expand-links)
 org-noter-arrow-horizontal-offset -30
 org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
 org-noter-doc-split-fraction '(0.67 . 0.9)
 org-default-notes-file "~/Syncbox/files/.notes"
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-file-apps '((auto-mode . emacs) ("\\.x?html?\\'" . default)
("\\.pdf\\'" . default) ("\\.jpe?g\\'" . "gqview -t %s &"))
 org-noter--pretty-print-location-for-title-hook
'(org-noter-pdf--pretty-print-location-for-title)
 org-odt-format-inlinetask-function
'org-odt-format-inlinetask-default-function
 org-ascii-format-drawer-function #[771 " \207" [] 4 "\n\n(fn NAME CONTENTS
WIDTH)"]
 org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-show-empty-lines org-cycle-optimize-window-after-visibility-change
                  org-cycle-display-inline-images)
 org-noter-auto-save-last-location t
 org-persist-before-read-hook '(org-element--cache-persist-before-read)
 org-noter--pretty-print-highlight-location-hook
'(org-noter-pdf--pretty-print-highlight)
 org-mode-hook '(#[0 "\301\211 \207" [imenu-create-index-function
org-imenu-get-tree] 2] er/add-org-mode-expansions org-appear-mode
                 #[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)
 org-babel-load-languages '((emacs-lisp . t) (ditaa . t) (perl . t) (python
. t) (octave . t) (shell . t) (matlab . t))
 org-appear-autoentities t
 org-noter--pretty-print-location-hook
'(org-noter-pdf--pretty-print-location)
 org-latex-format-drawer-function #[514 "\207" [] 3 "\n\n(fn _ CONTENTS)"]
 org-ellipsis " ↧"
 org-download-abbreviate-filename-function 'file-relative-name
 org-latex-format-headline-function
'org-latex-format-headline-default-function
 org-confirm-shell-link-function 'yes-or-no-p
 org-download-annotate-function 'org-download-annotate-default
 org-appear-autosubmarkers t
 org-adapt-indentation t
 org-html-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-download-screenshot-method "screencapture -i %s"
 outline-isearch-open-invisible-function 'outline-isearch-open-invisible
 org-odt-format-headline-function 'org-odt-format-headline-default-function
 org-appear-inside-latex t
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-babel-tangle-lang-exts '(("python" . "py") ("perl" . "pl")
("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-ditaa-eps-jar-path
"/opt/local/share/emacs/29.1/lisp/contrib/scripts/DitaaEps.jar"
 org-id-link-to-org-use-id t
 org-noter-headline-title-decoration "/"
 org-appear-autoemphasis nil
 org-noter--show-arrow-hook '(org-noter-pdf--show-arrow)
 org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
 org-html-format-inlinetask-function
'org-html-format-inlinetask-default-function
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-noter-arrow-background-color "cyan"
 org-odt-format-drawer-function #[514 "\207" [] 3 "\n\n(fn NAME CONTENTS)"]
 org-noter--add-highlight-hook '(org-noter-pdf--highlight-location)
 org-noter--get-current-view-hook '(org-noter-pdf--get-current-view)
 org-noter-arrow-foreground-color "black"
 org-noter-set-up-document-hook '(org-noter-pdf--doc-view-setup-handler
org-noter-pdf--pdf-view-setup-handler)
 org-noter--get-containing-element-hook '(org-noter--get-containing-heading
org-noter--get-containing-property-drawer)
 org-fold-core-isearch-open-function 'org-fold--isearch-reveal
 org-latex-format-inlinetask-function
'org-latex-format-inlinetask-default-function
 org-noter--convert-to-location-cons-hook
'(org-noter-pdf--convert-to-location-cons)
 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-noter--get-precise-info-hook
'(org-noter-pdf--doc-view-get-precise-info
org-noter-pdf--pdf-view-get-precise-info)
 org-noter--get-highlight-location-hook '(org-noter-pdf--get-highlight)
 org-occur-hook '(org-first-headline-recenter)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-noter--doc-approx-location-hook '(org-noter-pdf--approx-location-cons)
 org-link-parameters '(("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 :insert-description
                        org-info-description-as-command)
                       ("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)
                       ("attachment" :follow org-attach-follow :complete
org-attach-complete-link) ("id" :follow org-id-open)
                       ("file+sys") ("file+emacs") ("shell" :follow
org-link--open-shell)
                       ("news" :follow #[514 "\301\300\302 Q \"\207"
["news" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("mailto" :follow #[514 "\301\300\302 Q \"\207"
["mailto" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("https" :follow #[514 "\301\300\302 Q \"\207"
["https" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("http" :follow #[514 "\301\300\302 Q \"\207"
["http" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("ftp" :follow #[514 "\301\300\302 Q \"\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-noter-get-buffer-file-name-hook '(org-noter-pdf--get-buffer-file-name)
 org-html-format-headline-function
'org-html-format-headline-default-function
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-noter-get-selected-text-hook '(org-noter-pdf--get-selected-text)
 org-noter-create-session-from-document-hook
'(org-noter--create-session-from-document-file-default)
 org-startup-with-inline-images t
 org-download-link-format-function
'org-download-link-format-function-default
 org-return-follows-link t
 org-id-method 'ts
 org-download-image-dir ".figs"
 org-noter-create-skeleton-functions '(org-noter-pdf--create-skeleton)
 org-list-allow-alphabetical t
 org-noter-save-notes-at-end-of-session t
 )

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