It makes no difference to the original AR unit unless you cause a short circuit on those tracks. Use a separate DPDT switch in concert with the Wye turnout leading to the loco turnaround stub to flip the polarity to it. Just remember to flip the switch correctly every time. Be sure that that turnout is not of the power routing type and/or make sure the frog rails are insulated from other tracks leading up to it. The main power feed to the switch should be the reversing output side of the PSX-AR. You could also use a 2nd PSX-AR to power the turnout wye stub if the DPDT switch is too inconvenient. Just adjust the timing of the two units to not interfere with each other.
I have a reverse loop that is controlled by a PSX-AR and I have added a quarry at the end of this loop that is controlled by a wye. I understand that this creates another reverse loop but that I can manually control the turnout at the end of the wye using a DPDT switch. My question is: what does this do to the PSX-AR sensing functions - with or without another loco in the original loop?