I have two documents, docA with a bookmark1, and docB with an additional line and a new bookmark2. I open both documents and call docA.compare(docB) and save the result. The result document shows the insertion but bookmark2 is missing. Comparison in Word keeps both bookmarks.
Attached is the sample docx files and java class.
We have tested the scenario and managed to reproduce the same issue at our side. For the sake of correction, we have logged this problem in our issue tracking system as WORDSNET-22581. You will be notified via this forum thread once this issue is resolved.