A clarifying question...
You have one HDD with Win 7 and openSUSE 11.2, dual booting with Grub as the bootloader, chainloading the Win 7 bootloader? Since you have a maximum of four primary partitions, where do you have the FAT32 partitions? Are they logical partitions on an extended partition? Does Win 7 see them as part of the Win 7 installation?
If Win 7 sees them in its partitioning tool, you should be able to convert the FAT32 format to NTFS with the Win 7 partitioner without it making any difference at all. At the worst, you will have to repair the Win 7 bootloader with the Win 7 DVD. Grub should not be affected at all.
More detail would be of help and a copy of your partition table. As "su" in a terminal use the command "fdisk -l" and post back with the results.
Just to start you on your way in the new world.