How to get nested mapref's to display in TOC correctly?

If you open the ditamap in Arbortext Editor and then open the document using Edit > Edit Resolved Document for Styling, do you see a hierarchy difference in the topics referenced from the top most ditamap and the ref'd ditamap?

Ditamaps are containers of siblings, so a ditamap nested within a ditamap contains elements that are siblings to each other, and are also siblings to the content of the parent ditamap.

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There are a couple of tags that affect the nesting, topicref and topichead are two of those. In both of these cases if you do not want that parent topicref to provide output, you might want to set toc=no, print=no so outputs will notice the hierarchy change, but not try to output any headers or such.

There are other elements that may also provide this, but those are the most common.

Note that you cannot nest a mapref inside of a mapref in DITA as that outcome is undefined.