The risk of false calls of structural health monitoring systems is as much important for their application as their damage detection capabilities. Structural health monitoring based on guided waves propagation is particularly vulnerable to false calls. Signals acquired for piezoelectric transducer networks can be changed by many factors other than damage, for example, environmental factors or those related to the transducers’ aging or degradation of the transducers’ bonding with the monitored structure. A lot of studies were devoted to examine non-damage-related influences on structural health monitoring systems based on Lamb waves and to compensate the undesired effects. Most of compensation methods act on the level of the signal, that is, for a given factor influencing performance of piezoelectric transducers, signals are transformed to match the corresponding baselines. After such compensation procedure, the Damage Indices are calculated for the purpose of damage detection. In order to compensate the impact of all of non-damage-related factors, all of them need to be, at least, recognized. In this article, a different technique to compensate changes of Damage Indices values caused by factors other than damage is proposed. The method does not involve any operation on signals, but on the Damage Indices themselves. The factors causing Damage Indices’ changes neither have to be measured nor are even known. The capabilities of the method have been evaluated on the example of fatigue cracks detection in laboratory specimen tests and using results obtained during Full-Scale Fatigue Test of an aircraft.