I guess it depends how you installed in the first place. Did you use Mint4Win or did you do a standard install? If you did a standard install and you delete the the Mint partition then yes it will certainly interfere with your boot, you will lose both Mint and Windows. Not irreversibly, you will have to use Vistas tools or the windows command line to reinstate the windows boot loader before you got anything back. If you used Mint4Win first time around then I haven't got a clue what would happen as it is a complete unknown to me, my guess is you would be OK.
Two cd's and gparted showing your disk as entirely unallocated now that is a mystery. Do you have more than one hard disk? If so are you looking at the right one? Is your disk set up with LVM (logical volume management)? I am really clutching at straws here because I don't know the answer. I would be very reluctant to do anything to your installation until you find out why your disk is being read as unallocated. Have you tried Ctl/R from within gparted - this refreshes the devices (ie rereads them) It shouldn't be necessary but it might help.
Fujitsu Lifebook AH532. Intel i5 processor, 6Gb ram, Intel HD3000 graphics, Intel Audio/wifi. Realtek RTL8111/8168B Ethernet.Lubuntu 13.10,Ubuntu12.10 (Unity), Mint16 (Cinnamon), Manjaro (Xfce).