How best to archive MarginNote-annotated files?

All your notes can be converted based on the MN plugin.

We’ve been working on the instructions for these interfaces for the last few months, and have almost completed the main documentation, which we are now working on proofreading and translating into English for the community of developers. Introduction | MarginNote Addon Developing Guide (Preview Edition)
You will then have a high degree of data customization to suit the needs of different format conversions.