If you don't make a mistake and tell the Windows 2008 R2 installer to format the drives, your data should be safe.
If your D: and E: drives are formatted as traditional "basic disks", there certainly should not be problems.
If they are formatted as "dynamic disks", they should work in 2008 R2 too, although I'm not an expert on that.
(The Dynamic Disks seem to have been deprecated in Windows 2012, in favor of Storage Spaces. But I don't think a ML370 G4 will be a suitable platform for Windows 2012 anyway.)