I had similar problems. My grub loader randomly was erased, then i had a "hidden" partition somewhere out there. I tried to reinstall the grub bootloader, tried to use gparted, ended up losing data. I dont think any of this is really kali's fault, but the instructions are terrible. And because of the way I upgraded to win8.1 (win7 plus win8 upgrade) I have to go through that long process every time. Eventually I ended up with so many boot errors stating I had bad sectors and unrecognizable partitions, I gave up, and forked out the money for a new HDD. My way ahead is to use a dedicated harddrive for my multiboots so my primary boot is safe haha. (I understand it's really just some config that were pointing to the wrong place, but all that troubleshooting caused me to really screw up my stuff). Bottom line, needs better documentation (a central document, not the internet-document) and a better guide.
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