If you want to keep copies of your kindle books on your computer make sure that you use the 'transfer via usb' feature. At the moment, this only really works from the Manage Content and Devices part of Amazon.
There is a thread in the Kindle section of this forum discussing whether Amazon are phasing out this ability. Without it, you can only keep copies of your ebooks in the cloud. Hopefully, this is just a bug.
There isn't a way of transfering notes and highlights from your kindle to your computer then re-importing both the book and highlights. You can do this from Amazon's cloud storage (I'm not sure about the details of this because I always sideload books.)
You can save your highlights and notes from your books by using Kindle Mate.
https://kmate.me/
This is extremely useful.
Calibre works well with kindle books provided they are not DRM'd. If they are, google Apprentic Alf.