I was using a different version but I have now removed it. Still the
problem remains. The org version is listed as:

Org mode version 9.3 (release_9.3 @
c:/msys64/mingw64/share/emacs/28.0.50/lisp/org/)

On Sat, May 2, 2020 at 11:31 AM Eli Zaretskii <eliz@gnu.org> wrote:

> > From: Raoul Comninos <revcomninos@gmail.com>
> > Date: Fri, 24 Apr 2020 12:49:02 +0200
> > Cc: 40796@debbugs.gnu.org
> >
> > Yes, even if it is empty.
>
> Then I cannot reproduce this.  I made a .emacs file with only the
> following:
>
>   (require 'org)
>   (org-babel-tangle-file "~/.emacs.d/settings.org"
> "~/.emacs.d/settings.el")
>
> and then started Emacs 28, changed the default font, and saved the
> options via Options->Save Options.  Then I restarted Emacs, and Emacs
> was using the font I changed.
>
> Are you using the version of Org that comes with Emacs 28?  Or are you
> using a different version of Org?
>