Compile content issue

OK, I have a freaky problem and I could really do with some help to sort this out.
I use Scrivener on Windows and iPad now. I sync between the two with no problems on the whole.
I have an entire novel in Scrivener and have often compiled various versions in the past.

A short while ago I noticed that I seemed to have two versions of the entire novel in the same .scriv file.
One was a folder and the other a document, but they both contained the entire novel.
After looking at this situation for a while and doing some tests, I ascertained that they weren’t both the same thing, somehow mirrored, but were two copies of the whole thing.
The document version I decided to delete. I found that I could not delete it at the document level, so I deleted all the contents.
Since that point, I have ignored the now empty document in the Binder and have continued to work on the other version in the Folder.
You can seee these two versions in the screenshot, the lower one is the one I work with. versions.JPG
Now I come to compile the thing and find that Compile seems to think there are no contents to the entire folder.
But there are - as you can see in the screenshot.

Now I’m really not sure what to do next. I’m nervous about losing the whole thing but I really need to compile.
What can have caused this situation and how do I get out of it?
Thanks everyone.

Just remembered something - this duplication occured after I upgraded to the most recent version of Scrivener.

OK, I solved it!
Following a brainwave I copied all the contents of the second Folder into the first Document.
Now the content is there for compile.
I deleted the Folder, which was obviously the problem.
All sorted.