As mentioned, she is correct - on the plus side , if upgrading the whole way, it will only count as a single flight for upgrades and the number of upgrade credits will be that for the distance of the journey, rather than 2 sets of upgrade credits being needed
MCI-PHX plus PHX-RNO would seem to require 3+2 = 5 upgrade credits ( 1044mi. plus 601mi, ) whilst MCI-RNO on the same flight number would require just 3 upgrade credits since MCI-RNO is approx 1337 mi.