I suspect this has been answered before -- if so, I apologize.

Flying SAN TO DCA in a couple weeks. Stopping in IAH but same flight number.

Tried to apply RPU. R class is available SAN to IAH but not available from IAH to DCA. Agent told me that they cannot confirm one segment when it is a through flight with same flight number. They must be able to confirm the whole way.

Is this true? Is there a way to do this?