We've been affected in the past, when we innocently upgraded with miles to the last row or two in the larger FC cabin ...
When a smaller FC cabin is substituted, the downgrades from FC to Coach begin with the last FC rows (the one's missing from the smaller aircraft) ... but only for mileage/certificate upgraded seats. So anyone on upgraded or free (mileage or certificates) gets bumped starting from back to front --- while they try to keep paid FC up front. My wife and I have received vouchers worth a few hundred dollars for future flights on the few occasions where this downward bump has occurred.
I'm not sure what they would do if everyone up front is paid FC ... but folks with refundable FC tickets would certainly have more leverage.
As mentioned in an earlier post, my wife and I learned to book as close to the front as possbile when upgrading to FC ... and under these circumstances we have never been bumped from these seats.