Hi,
Org removes all overlays when calling org-babel-execute-subtree. Here is a way to reproduce: #+begin_src elisp (with-temp-buffer (let (ovl (statuses nil) (live-p (lambda (xo) (or (and (overlay-buffer xo) "alive") "dead")))) (insert "* Mandatory heading") (org-mode) (setq ovl (make-overlay (point-min) (point-max))) (push (list "before" (funcall live-p ovl)) statuses) (org-babel-execute-subtree) (push (list "after" (funcall live-p ovl)) statuses) (nreverse statuses))) #+end_src #+RESULTS: | before | alive | | after | dead | Org should not remove overlays it doesn't own. After investigation, it seems that any use of `org-save-outline-visibility' will call: (org-fold-core-region START END nil) ^^^ which will, indeed, remove any overlay (except for those that are both 'org-invisible and 'invisible). Thanks, Bruno Emacs : GNU Emacs 30.0.50 (build 1, x86_64-pc-linux-gnu, X toolkit, cairo version 1.18.0) of 2024-03-12 Package: Org mode version 9.7-pre (release_9.6.20-1281-gfb61e8.dirty @ /home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/) current state: ============== (setq org-yank-image-file-name-function 'org-yank-image-autogen-filename org-persist-before-write-hook '(org-element--cache-persist-before-write) org-html-format-headline-function 'org-html-format-headline-default-function org-html-format-drawer-function #[514 "\207" [] 3 ("/home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/ox-html.elc" . 24162)] org-latex-format-inlinetask-function 'org-latex-format-inlinetask-default-function org-speed-command-hook '(org-speed-command-activate org-babel-speed-command-activate) org-persist-after-read-hook '(org-element--cache-persist-after-read) org-confirm-elisp-link-function 'yes-or-no-p org-latex-format-headline-function 'org-latex-format-headline-default-function org-latex-format-drawer-function #[514 "\207" [] 3 ("/home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/ox-latex.elc" . 37582)] org-mode-hook '(#[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-confirm-shell-link-function 'yes-or-no-p org-odt-format-headline-function 'org-odt-format-headline-default-function org-archive-hook '(org-attach-archive-delete-maybe) org-metaup-hook '(org-babel-load-in-session-maybe) org-occur-hook '(org-first-headline-recenter) org-html-format-inlinetask-function 'org-html-format-inlinetask-default-function org-ascii-format-drawer-function #[NON PRINTABLE] org-bibtex-headline-format-function 'org-bibtex-headline-format-default org-link-parameters '(("attachment" :follow org-attach-follow :complete org-attach-complete-link) ("id" :follow org-id-open :store org-id-store-link-maybe) ("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) ("file+sys") ("file+emacs") ("shell" :follow org-link--open-shell) ("news" :follow #[ ---NON PRINTABLE--- ] ("/home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/ol.elc" . 52731)] ) ("mailto" :follow #[ ---NON PRINTABLE--- ] ) ("https" :follow #[ ---NON PRINTABLE--- ] ) ("http" :follow #[ ---NON PRINTABLE--- ] ) ("ftp" :follow #[ ---NON PRINTABLE--- ] ) ("help" :follow org-link--open-help :store org-link--store-help) ("file" :complete org-link-complete-file) ("elisp" :follow org-link--open-elisp)) org-persist-directory "/tmp/org-persist-6fkhMh" org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-metadown-hook '(org-babel-pop-to-session-maybe) org-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org--warnings nil org-babel-pre-tangle-hook '(save-buffer) org-export-before-parsing-hook '(org-attach-expand-links) org-link-shell-confirm-function 'yes-or-no-p org-fold-core-isearch-open-function 'org-fold--isearch-reveal outline-isearch-open-invisible-function 'outline-isearch-open-invisible org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-agenda-loop-over-headlines-in-active-region nil org-link-elisp-confirm-function 'yes-or-no-p org-odt-format-inlinetask-function 'org-odt-format-inlinetask-default-function 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-persist-before-read-hook '(org-element--cache-persist-before-read) org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default org-odt-format-drawer-function #[514 "\207" [] 3 ("/home/bruno/work/open-src/emacs/orgmode/orgmode/lisp/ox-odt.elc" . 18494)] )