Bruno Barbier <brubar...@gmail.com> writes:

> Org removes all overlays when calling org-babel-execute-subtree.
> ...
> 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 for reporting!
Fixed, on bugfix and main.
https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?id=8b73c8b98
https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?id=712ef988c

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

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