Solution
The Windows OS for PXI controllers is no different than a normal Windows OS for a desktop PC, so if you are looking to reinstall the Windows OS, you can use any Windows OS media for the installation. If you do this, then be sure to also install the peripheral media needed for the PXI controller. Firmware and peripheral drivers are available as downloads; search by model name to find the relevant software.
NI also sells recovery media for some PXI(e) controllers. To check whether recovery media is available, visit the NI PXI Advisor. If recovery media is available for your controller, then it will be displayed under the "Options/Accessories" for the controller within the advisor.
Note: Recovery CDs are no longer sent out with Windows 10. All Windows 10 recovery information and images can be found online. Alternatively, you can purchase a Windows 10 IoT Enterprise USB Recovery Media For PXI (PN: 787269-03) from NI.