I am using the MergeDocx extension to process altChunks in a word package.
Here is my code to inject altChunks
PartName partName = new PartName("/test.docx");
AlternativeFormatInputPart afiPart = new AlternativeFormatInputPart(partName);
afiPart.setBinaryData(new FileInputStream("C:\\Temp\\segment.docx"));
ContentType contentType = new ContentType(
"application/vnd.openxmlformats-officedocument.wordprocessingml.document.main+xml");
afiPart.setContentType(contentType); // docx
Relationship altChunkRel = mainPart.addTargetPart(afiPart);
CTAltChunk ac = Context.getWmlObjectFactory().createCTAltChunk();
ac.setId(altChunkRel.getId());
// Get Body content array of objects
aBodyContent = mainPart.getJaxbElement().getBody().getContent();
// Spin thru all content controls and locate this segment
for (int i = ...