Hi there,
You still have not answered my question about how you are loading the document after its been downloaded. Are you using the rest API to extract and load annotations when a document is loaded? What does your document loading code look like?
The reason this happens is usually because the annotations are being loaded twice - the ones baked into the document from the merge operation that you are doing, and another time when you load the document and extract and import the XFDF.
If you are using the rest API to extract and load annotations, then you need to provide the disableFlattenedAnnotations option.
Thanks,
Logan