Model based Fault Detection and Isolation (FDI) in aerospace have received considerable attention and numerous algorithms are flying on-board commercial aircraft. Most of these algorithms are based on local models of aircraft components or rigid body aircraft models. On the other hand the ever more pressing requirement of performance and fuel efficiency improvement makes aircraft structures more lightweight and flexible. Actuator fault detection especially ailerons in the wing has to account for these flexible effects to provide the required performance. Within the article we show the trend how decreasing detection time necessitates the use of flexible dynamics based FDI, and show how detection and isolation performance are changing. Moreover, the article also highlights the need of robust filter synthesis methods, since a nominal H∞ synthesis has significantly lower performance in worst-case situation than a robust µ synthesis based filter. The methods are demonstrated on a flexible aircraft demonstrator platform simulation model from the FLiPASED project.