I figured it out. Don't use anchor tags. Instead:


### B

[]{ref1}Bar, Foo. What a mess!

### F

[]{ref2}Foo Bar. See [Bar, Foo](#ref1)


If this is in the docs I never found it. The downside to this is that the 
links don't work in a standard markdown editor. If Pandoc can handle this, 
it ought to handle using HTML anchors the same way. There's no need to 
require special formatting here.
On Monday, December 28, 2020 at 3:51:46 PM UTC+1 Gary Glass wrote:

> Here's the deal: I am converting markdown to epub. One of the markdown 
> files is pretty big, but it's broken up into various level-3. There are 
> many cross-ref links among the items on the page. e.g.:
>
> ### B
>
> <a id="ref1">Bar, Foo. What a mess!
>
> ### F
>
> <a id="ref2">Foo Bar. See [Bar, Foo](#ref1)
>
>
> But since the file is pretty big I use epub-chapter-level=3 to split it up 
> into small chunks in the epub output. But doing that breaks the cross-ref 
> links.
>
> What are my options for getting this to work?
>

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