According to your nickname, you should have already lived long enough to know all answers.
The books are on your Amazon account cloud.
Read the pop-up more carefully next time:
It says:
"Remove from device"
It does not say:
"Delete from device"
It will only say 'Delete' for item that are not backed up on the Account cloud.
The sidecar directory remains behind to save any user added information (bookmarks, quotes, indexing, whatever) for the next time you bring it onto the device.
Calibre is not checking your cloud account nor the information on your Kindle to see what the actual status of the book is.
Translation:
Get Calibre fixed or always consider its limitations.
The developer's sub-forum here has a script posted that will clean up your Kindle for anything that is no longer present on it.
Last edited by knc1; 07-09-2017 at 08:57 AM.
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