Arnold
My understanding is that the HW hardware trigger mode is controlling the A and B channels of the ADC. It is not controlling the A/B MUX of the input pins connected to the A/B channels, which is controlled by ADC0_CFG2.
Therefore, if you consider the two ADC inputs ADC0_SE5a and ADC0_SE5b you can connect them to an ADC channel by selecting ADC6a or AD6b in SC1n[ADCH] but the physical pin is still connected to either the a or b pin, depending on the ADCx_CFG2[MUXSEL] bit.
If you look at the table 3.7.1.3.1 ADC0 Channel Assignment for 144-Pin Package (for example) there is a foot-note (number 5) for such inputs which states: "ADCx_CFG2[MUXSEL] bit selects between ADCx_SEn channels a and b. Refer to MUXSEL description in ADC chapter for details".
Therefore I believe that two settings need to be changed (channel and MUX) each time these are switched between.
Regards
Mark