Not solved 100 %, but there is 2 ways to solve this.
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Install Plugin “Better Markdown Links” Better markdown links. Then install the open-source markdown editor QOwnNotes together the plugin “Import and Converter”. Just press the button “GFMExport” (githubflavouredmarkdown export). All you notes are converted to github markdown. You can also convert it back to Obsidian Format.
GitHub-friendly header links - #4 by netlimpopo -
Export your notes with export tools into standard markdown format:
There are Obsidian Plugins such as “Obsidian markdown export” or there is also a commandline tool Obsidian Exporter “https://github.com/avcton/obsidian-exporter“ . Another Commonmark Exporter: GitHub - zoni/obsidian-export: Rust library and CLI to export an Obsidian vault to regular Markdown .Note that in Obsidian there are no unique headings yet. So links can’t be 100 converted as Obsidian right now has no concept of it to make those connections in the first place (see QOwnNotes Obsidian Import ).