Yeah, but you lost me then. Either Markdown is the source of truth (and you do the CRDT when one is edited and reconstitute it after) or I won't store my notes in your app :)
I've heard that CRDT needs to be the source of truth for certain features to work (handling users going online/offline?). I was never quite sure why it would not work to just create a new CRDT document from another source of truth (markdown, database, ...) when starting an editing session. Maybe someone else can explain.