Don't merge the folder. The files inside also have to have the appropriate names.
Just rename and move the azw3 from the Rothfuss, Patrick folder to the documents folder. All will be well.
It's all right, this issue is very thick, so it's not you. This is a lot of confusing arbitrary indexing stuff, and it took me a while to pick up on it too. Although I am always open to giving instructions.
It is 100% certain, I have 300 books like that on my kindle right now, so you came to the right place.
(Also, it's not the DRM that has the features, it is the Kindle software and format.)
Also, the cover is not stored in the sdr, it's actually in E:\system\thumbnails\ which is a system folder (hence the name) so you will have to perform some settings-fu to view it... or just type it manually into the address bar.
And the covers only depend on having the right ASIN in the filename, so they will match all books with that filename (there should only be one....)