Hi Ali, welcome to NST.
If you delete the boot folder, the system will no longer be able to boot !
It contains the BCD, which holds the information about the location and type of each of your systems.
To boot Ubuntu you must use
EasyBCD 2.0 for any Ubuntu after 8.04. Make sure that you use the "advanced" button during Ubuntu install to prevent the default action of Grub replacing the Vista boot. Tell it to install grub to the Ubuntu partition boot sector.
In EasyBCD Go to "add/remove", click the Linux tab and select the partition where Ubuntu (and grub) is installed.
If Ubuntu is on the
same HDD as Vista, that's all you need.
If Ubuntu is on a
different HDD, you'll need to tick the "grub is not installed..." box, which will then cause Neogrub to be installed as a link to your Ubuntu disk.