OK, that's making sense. I can see all my pdfs (documents). I'll have a play and see if I can download them and transfer to Evernote. Maybe keep Kindle app just for Amazon purchases.If you go under your Amazon account and manage your device:
https://www.amazon.co.uk/mycd
You will be able to download your PDFs (not the books or other stuff bought via Amazon).
It is a bit fiddly to use, maybe if you move them into a collection first, it will be easier to select them all at once later on from the web interface.
I just tried and I can download the books and PDFs that I manually added to my Kindle.
See if it works for you, not 100% sure as you are using the "print to kindle" function.
I used to send digests and copies of longer online articles I wanted to read on my Kindle via Instapaper, and those are not downloadable weirdly.
Appreciate the help.