I don’t know if you ever got to the bottom of this problem. I had a similar experience today - but I found that the problem arises only when using Word files in .doc format, not .docx.
A colleague edited my document in Word and returned it to me in .doc format. When I opened the edited document in Word, the references all still contained valid links to the citation on paperpile.com. The Paperpile links were retained when I opened the document in “Office Compatability Mode” in Google Docs. But then, when I selected “Save as Google Docs” in order to continue editing, all the Paperpile links were replaced by http:///h .
So I then tried opening the .doc file in Word and saving it in .docx format. When I opened the .docx file in Google Docs and selected “Save as Google Docs”, the Paperpile links were retained.
Now that I’ve figured it out, this is amazing functionality to have. I can now continue working on my paper in Google Docs, adding/changing references with Paperpile, even though the earlier version was edited in Word. Thank you!