Using the "Open XML Performance Tool", I analyzed the structure of the docx document and came to the conclusion that merging documents with their style, headers, footers ... is impossible from the box using Altchunk. You can download the tool separately from open xml sdk .
What I am doing now and what works is copying everything manually into a document, making sure that all style links, link headers, footers ... are saved. This means that I give them a new unique identifier before copying them into a document and changing all links from the old identifier to the new one. There is a lot of code for this, but the tool mentioned above really helped.
. , SectionProperties -tag SectionProperties -tag Body -tag, . , , SectionProperties -tag SectionProperties -tag Body -tag. .