Issue when importing the .md file from Dropbox

I made some progress but I still cant the sync to work well enough.

I downloaded the md files that were synced to dropbox to a new machine

However the files are individual files, not directories. I can only import them one at a time to jolpin which isnt feasible with thousands of files. Using the file system type sync option there is no option I see to sync directories, only individual md files!

is that correct?