Problems organizing

I’m not sure whether this is related to Feed Organizer problem and feature but I am having great trouble organizing feeds. After a couple of attempted cleanups, exporting the OPML and editing that to get rid of duplicates, I deleted everything and re-imported what I thought was a cleaned up list of feeds organized in folders. However, all the old folders were still there and now there seems to be massive duplication of feeds within folders.

So, here is a screenshot of my Organize

and you can see there is a single entry for Article-Mother Jones with 2 opens.

And here is a screenshot of the Links, the folder in which that feed should be, showing 4 copies of that feed.

Some other feeds there are only three. I haven’t checked them all.

I would really like to clean things up better, because it makes keeping feeds organized easier in future. So I guess my question is, can I simply delete all except one copy of the feeds in each folder?

Ideally, I do not really need a top level at all, if that is possible.