I think I fixed it.
Kindle continued to connect very very slowly without any error message. So I tried to manually initiate scan in windows with both options checked (I don't know what they are called in English). And for now everything seems back to normal. I just need to remember to safely remove hardware - The quickest option seems to be to right-click the drive in explorer and press eject (tray option takes 5 seconds and Calibre eject only ejects from program processes I think)
The fault was interrupting upload process and I don't know how it happened in the first place (it froze on upload) but it might be due to loose cable.
Back to using Kindle and Calibre problem-free =)
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