Problem with partion resulting in "One of the source volumes specified has an invalid format and cannot be protected using Windows Backup. Only volumes formatted with NTFS/ReFS can be protected."

We have two new Windows Servers 2012 R2 that I'm trying to set backups on using a script. When I used the -allCritical switch, I get the error specified in the subject. When I look at the partition information using diskpart, I see a 2048 MB partition with no drive letter labeled as System that is FAT32. I was never prompted to my recollection of what file system to format the partition with. Is it safe to assign this partition a letter, convert to NTFS, and then remove the drive letter?

Thanks