I think chetana's boot partition is the /boot partition commonly used in the Red Hat family.
The removal of /boot will cause Windows unbootable but Windows MBR can be restored with installation CD like Lenard already described.
The MS systems use a common MBR and so booting up a DOS 6 floppy with fdisk.exe inside and type
will achieve the same result.
Thereofre just use Winddows disk management to delete the /boot partition.