Ion migration in high repetition rate femtosecond laser inscribed waveguides is currently being reported in different optical glasses. For the first time we discuss and experimentally demonstrate the presence of two regimes of ion migration found in laser written waveguides. Regime-I, corresponds to the initial waveguide formation mainly via light element migration (in our case atomic weight < 31u), whereas regime-II majorly corresponds to the movement of heavy elements. This behavior brings attention to a problem which has never been analyzed before and that affects laser written active waveguides in which active ions migrate changing their local spectroscopic properties. The migration of active ions may in fact detune the pre-designed optimal values of active photonic devices. This paper experimentally demonstrate this problem and provides solutions to avert it.