Hi Ralf,
If I understand your question correctly, you want to change the FIR filter on AD9361 while you are using the chip (transmitting or receiving for example). One thing you can consider is to use the "Coefficients to Target" function of the filter wizard. In this way, even if your chip is being used, you can adjust the FIR parameters. However, you need to take the initiative to design a new filter. The filter wizard does not have the intelligence to sense the environment and adjust the filter settings dynamically.
Thanks,
Di