Choose the folder, not a single note

  1. Locate the folder in Finder and make a backup if it contains important work.
  2. Choose File > Open Notes Folder or press Command-Shift-O.
  3. Select the folder and check the sidebar for the files you expect.

When the folder looks empty

Check the selected path and file extensions. A folder elsewhere on disk is a different folder even if its name matches.

The folder has no MarkThatDown sync account

MarkThatDown does not create a sync account. External synced folders remain subject to the provider’s availability and conflict handling.