I am currently scheduled to fly CDG-PHL-BOS on 11/19 on award travel. Something came up and I now have to be in Houston on 11/19 also. If I fly to BOS as scheduled I will arrive too late to catch any flights to Houston, so I am looking to book PHL-IAH on 11/19.

Now will the reservation computer see that I am confirmed on 2 flgihts on different itineraries on the same day and cancel one of them, or can I check into both flights and just not show up for the PHL-BOS leg?

The system won't cancel your PHL-IAH segment, but it may cancel your return flights (if any) when you skip the PHL-BOS segment.