The way to test is to use the switch from internal to external clock on EtherRegen while it’s running in either mode.
Pull the power plug in and out. So you have approximately only 5 seconds in loss of music switching between the alternatives.
The extra ports in use on A side shouldn’t affect the outcome of B, which you’re testing. Clocks is located B side. This is also why B>A may not be as good as A>B when an external clock is in use, as the clock will have added extra phase noise crossing the moat.