added -Wundef to the build  https://gcc.gnu.org/onlinedocs/cpp/If.html
without it the following code will not issue a warning

//#define PIGS 1
//#define DOGS 2

#if (DOGS == PIGS) not detected without -Wunded
#warning("DOGS == PIGS")
#else
#warning "DOGS != PIGS"
#endif
will not issue a warning (other than the pragma) and PIGS == DOGS is
true
Fixed my merge error and found that both BOARD and PX4FLOW have been
undefined in the build.
So the #if was not doing what was expeced.
As it turned out to be not needed as both F4's use the same alternate
functions DM,DP and VBUS