It is not possible to use a NI-made RMC board like the 9694 and a custom-made RMC board which implements an additional serial port at the same time. This is why your socketed clip option disappears from the project after adding the 9694. The 9694 uses that RMC IO so it can no longer be accessed via a socketed clip.
However, additional DIO can be implemented on a custom RMC board that also includes a serial port. You can read more about implementing ASLR:2 and DIO on your board in the RMC Design Guide.
You could also use the 9694 along with an external serial transceiver board, like this digilent product: https://store.digilentinc.com/pmod-rs232-serial-converter-and-interface-standard/. In this case you would not add the 9694 to you project. Rather you would create your own CLIP with the sbRIO CLIP Generator that implements ASLR:2 on pins of your choosing, which should be routed out the 9694. As long as you connect the external serial transceiver to the 9694 correctly you should be able to access the serial port as if you had implemented one on a custom RMC board.