Workflow using Calibre

Calibre seems like a good solution to create PDFs to work with in MarginNote (e.g,. from Kindle books), at least for those of us with access to a Windows PC. Then, the PDF is in the Calibre library. Calibre also seems to be a reasonable solution as a library for PDFs.

I’ve read a number of posts but am unclear about whether there is a safe way to keep the PDF in Calibre synced with the annotated MN3 file.

For now, should I just accept that the safest process is to make a copy of the PDFs stored in Calibre to a cloud drive and import the copies into MN3? Or is there a better, safe workflow?

It appears that there is some risk of corrupting the Calibre database so, of course, I would like to avoid that.

Does anyone have a workflow using Calibre and MN3 that is working for you?