It depends on the actual fare basis of the ticket you purchased, and how fares may have been combined to get your routing.

I was recently looking at EWR-IAH-PVR (Puerto Vallarta), and for connections on the RJs IAH-PVR, which booked in Y, the itinerary was pricing out cheaper than a connection on the one daily mainline IAH-PVR flight, which booked in R. So in that case, you wouldn't have been able to switch to the mainline flight in FC without an increase in fare.

Unless you printed out the full fare rules for your ticket, which may be a combination of several fares, you'll have to contact CO to get the answer to your question.