Bootcamp partition on second drive

I have two drives on my imac, a ssd and a 1TB second drive, the mac os and applications are on the ssd, the second drive is formated in HFS has my itunes folder and also has my windows 7 bootcamp partition. If i reformat the second drive into fat32 will it harm the working of the mac side, and will re-formatting mean i need to re-install windows.