No, I didn't have the folders on my laptop when I started syncing and then when the issue started and I checked the selective sync settings, those other sub-folders which caused the sync issue were not selected, which I was so confused.
Now I have my old laptop back (it was at repair) where obviously the sync issues pulled through, and now when I check the selective sync settings, those folders are indeed selected.
I guess I can try and delete the duplicate subfolders that are now in the main folder as selective sync issues. Do I understand correctly that the best way to do this is to delete the conflicted sub-folders (which are now appearing as primary folders) on the Dropbox cloud - which will not delete the subfolders in the original folders and will hopefully also remove this from my laptop?
If you have two versions of the folder in your account online, I'd suggest making sure that they're consolidated, and you're not missing files from the original folder before deleting the conflicted folder.
Any changes you make in your account online should then sync to your computer too.