I have a client using R1Soft Continuous Data Protection backup, and two of the Server 2008 R2 boxes were erroring out with these errors:

Unable to obtain NTFS volume data for device '\\?\Volume{f612849e-7125-11e0-8772-806e6f6e6963}': Incorrect function.
Unable to discover information for filesytem volume '\\?\Volume{f612849e-7125-11e0-8772-806e6f6e6963}'; Unable to obtain NTFS volume

So I backed up all the registry entries with this, {f612849e-7125-11e0-8772-806e6f6e6963}, in it, and deleted them based on some VERY sparse info from R1Soft. I then decided to restore them before I rebooted, and do a system state backup first using MS backup, and even it errored out saying that there were FAT32 partitions.

This was a major clue as the only two computers with problems had these FAT32 partitions. I figured if MS backup can't backup something, any other program is likely to have problems. Also, now that I realized the servers had FAT32 partitions on them, the error referencing NTFS takes on more weight. The partitions on both servers have the label "OS", but on one of the computers, it is given a letter, but on the other not.

So I am thinking if I just convert the file systems from FAT32 to NTFS, it may solve the backup problem. So the question is this: Can I just convert those partitions, and does anyone have any concrete knowledge of any major downsides, like the servers not coming back up (of course, I would do one at a time)?

My thinking is that the answer is probably at least 95% no, but they are production servers, so I wanted to get some second opinions.