To give an update, I started using Empirical Mode Decomposition which for my case seems to be more promising since I can easily replace data.
[imf,residual,info] = emd(data,'Interpolation','pchip');
As you can see IMF1 data has a varying frequency and constant frequency component. Is there a way to make adjustments to the first sifting stage?
The problem is the main part of the faulty signal is contained in IMF1 but is needed in IMF2 - seperated from the constant signal.