Briefly, the answer is yes. Decrease in the absolute fluorescence intensity is completely normal during switchSENSE® experiments. There are several factors that can affect the fluorescence emission, for instance photobleaching, chemical and thermal stress on the fluorophore, loss of DNA from the sensor surface or quenching of the fluorophore by a hybridized protein conjugate. So, do not worry about loss of fluorescence intensity between regeneration steps. When you observe an increase in the repulsive fluorescence intensity (Fup) during the respective hybridization, the sensor electrodes are successfully functionalized.
For further reading, please also refer to “What is a chip regeneration? How do I know, if my chip regeneration was successful?”.