Second-system effect is the replacement of a full production application with another full blown production application where the second-system has to replicate all (or at least most) of the features from the first-system into the second one while also adding new features into the second-system. Even worse are the cases where the first-system still has to coexist and keep being developed while the replacement second-system is in development, that usually leads to a never-ending catch up of the second-system trying to integrate all the changes from the first-system that happened after the start of the second-system project.

Have you read the book? I'd recommend it!