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I was trying this for a while, but the inability of labeling and refering to specific math equations became a deal breaker.

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I might be wrong but you'd need to install pandoc-crossref and add it as a filter in Zettlr, somewhere in the pandoc preferences. Then use pandoc-crossref's syntax on the equations.

https://github.com/Zettlr/Zettlr/issues/1966

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