Converting System Reserved from FAT32 to NTFS on a Windows Server 2008

I have a Windows 2008 Enterprise server (SP2, not R2) OS and I discovered (to my horror) that a previous administrator had setup the system reserved partition using FAT32.  This is my main web server and FAT32 systems are not allowed on my company's domain. Here is the Disk info:

C:\  Partition (NTFS) - 1TB - Main Windows partition - 70% free
F:\  Partition (FAT32) - 1.3GB - Reserved System partition

I think I need to create another NTFS partition and move system reserved this new NTFS partition.  However, I've never done this before and I'm not sure how to proceed.  I have a feeling it's not as simple as copying files off the existing partition, formatting the partition to NTFS, and then copying the files back.  I don't want to hose this server and re-installing Windows is not an option.
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Lee W, MVPTechnology and Business Process AdvisorCommented:
BEFORE YOU DO THIS - I would recommend you post a screen shot as that might be a Windows Partition.  It may be removable, or convertable, but posting a screenshot should help us know for certain.

More information:

And if you want to convert a FAT file system to NTFS - ASSUMING YOU ARE CERTAIN THIS ONE IS NOT CRITICAL TO WINDOWS - simply type CONVERT X: /FS:NTFS where X is the drive letter you want to convert.
Leave it as it is. That partition isn't being used, or only during bootup or for diagnostic purposes. Usually it also includes diagnostic utilities which are DOS based, and those tools wouldn't work if the file-system were NTFS. It also doesn't (or shouldn't) have a drive-letter assigned, to make it inaccessible to the OS.
noxchoProduct ManagerCommented:
Apparently this was done not by your system administrator but by server provider. You can easily convert it using a command suggested by leew. I've never had problems in doing so.
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No, as I said, leave it as it is. Older servers, for example Dell and HP servers, when correctly setup, use this partition for diagnostics, and for the diagnostics to be able to run the partition must be FAT. If you convert it, you loose that functionality.
progismapsAuthor Commented:
I CANNOT leave it as it is.  FAT32 was identified as a security risk and I'm not allowed to have FAT32 drives on the exceptions.  I either have to reformat as NTFS or move it to a NTFS partition.   Re-installing Windows is a HUGE nightmare that I don't want to do.  Since this drive contains boot information and I can assume it is critical to Windows.

Disk Management Screenshot
Remove the drive letter, it doesn't belong there. Without a drive letter there is no security risk. It is part of a proper server installation on older hardware. Not leaving it as it is is a bigger risk. Get your superiors to understand that.

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noxchoProduct ManagerCommented:
How much used space is in F partition? And what is inside? As said - you can convert it which I did on Dell servers and I never saw any problem after converting them to NTFS.
You can backup this partition then convert it and see if you get any problem. If yes then restore it back. If not - leave it ntfs.
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Windows Server 2008

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