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.
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
)