I do this regularly. French citizens can have 2 passports, a facility I have been using for 2 decades. Only once have I been asked about the discrepancy – and that was not about the number I input in the reservation – Immigration usually doesn't have that information – but because the officer in country B couldn't find the exit stamp from country A. I showed him my other passport, he saw the stamp, and saifsaid "Okay!".