Hi Kurt,
The contact center software would need to be re-installed after the Windows upgrade.
In this specific case, where you are upgrading from Windows 2003 which is 32-bit to Windows 2008 which is 64-bit, the Windows installation is basically a wipe and replace. So, when you describe an "in-place" upgrade, if your hope is that you could upgrade the Windows and there would be no other impact to the system, that is not the case.
Jim