the partition was automounting and Windows was trying to assign a drive letter. Had to disable automount, the manually formatted the linux partitions in Windows and then deleted. It was not straight forward but eventually got it deleted.
By the way, Do you have any Live CD with any Linux distro?
If yes, can you try booting with it and see whether that helps in getting rid of the partition?
Or should I go your way. Disable automount and stuff
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