Solution
Ethernet, CAN, RS-232, RS-485, and RMC processor peripherals created using the CLIP generator are all are routed through the FPGA. These peripherals will be temporarily unavailable when the FPGA is reconfigured. Downloading your FPGA application to the flash of the sbRIO ensures that the FPGA is configured before the driver can access a given peripheral.
Once you recompile the FPGA, you should be able to find your peripherals created.