It turns out that the document root namespace does not get passed to the XPointer parser that is invoked as part of the expansion of XIncludes, so specific TEI element names were being read as in the empty namespace. Added a tei: prefix definition to the XInclude elements and used the prefix before every element, and now they work. Hurrah. Discovered this by looking at exist.log on my local version of the db, at AR's suggestion on the eXist list.