@peregrineay your solution (copy subfolders, selectively unsync, re-import subfolders) made sense to me but it hasn't worked for me, unfortunately.
Once I had un-synced the folders, I then re-imported the folders and Dropbox immediately added them again. The folders are now called .Rproj.user (Selective Sync Conflict) and .git (Selective Sync Conflict). If I unsync them again, they will just be removed from my local machine again.
Because Dropbox is now syncing the reinstated folders again, this won't solve my problem which is outlined here: The process cannot access the file because it is being used by another process (and here)