Thought you might be interested to know that, after chatting with the Hypothes.is folks and perusing this post on how Hypothes.is interacts with document metadata, I was able to "migrate" Hypothes.is annotations as I migrated my Ed instance to a new server.
I modified the _include/head.html to include DC metadata using Dublin Core tags with name attributes in addition to the Zotero-friendly property attributes. I also included a few site wide entries in _config.yml. As a result Hypothes.is associates annotations with a urn:x-dc: string rather than the URL.
If it sounds useful to other users, happy to issue a pull request.