With just a simple command in Windows, though, you can actually convert a FAT32 drive to NTFS without reformatting entirely (and thus losing all your data).

Plan on using the command line:-convert drive_letter: /fs:ntfsTo convert a fat32 drive to ntfs. I plan on doing this to about 50 PC's and was wondering if there is anything I should be aware of ...

I'm not really familiar with NTFS and it's benefits. I've tried the search function and i found a command line operation to convert a partition to NTFS (i think).