If FSW (the sensor modulation frequency or switching frequency) is selected such that CSENSOR is fully charged and discharged, then RSERIES values do not affect raw or difference counts of sensor measurements. In CapSense systems, series resistors are used to filter out EMI and reduce radiated emissions. Cypress recommends typical RSERIES values to be 560Ω.
For the sensors to fully charge and discharge to required voltages in every switching cycle, the period of the sensor modulation signal (1/FSW) should be greater than 10 * RSERIES * CSENSOR. So, if the RSERIES value gets so large that it start to filter out the sensor modulation signal enough so that the sensor is not fully charged by the modulation signal, the difference counts begin to decrease when the RSERIES value increases. Note that this is not a desired behaviour. If your sensors are not fully charging and discharging properly it is recommended to decrease the switching frequency by using prescalar configuration and putting proper prescalar value. (1/FSW>= 10 * RSENSOR*CSENSOR)