The good news:
A full set of 25 documents successfully generated a new version as part of the multi-doc generation.

The bad news:
It appears that Element Reports aren’t being generated when the document is regenerated in this way.

I have two very simple Element Reports in each document; one that pulls out a single Action from a single package and display just the Description. Another which pulls out a set of Actions from a package and displays the Name as a column and the Description as another column.

Both reports work without issue when regenerating a single document.