Guys, is there code section that prohibits neutrals from two different panels being tied together? I figure there has to be, but I don't know the section that would apply here. The issue at hand is using a spdt relay to transfer load from a normal panel to an emergency panel. I think you would need a dpdt relay for this.
This is more complicated when you have the situation of a transfer switch controlling to different sources, such as POCO and generator. There you may have the choice to treat the generator as a separately derived system and switch the neutral or treat the generator as non-separately-derived and bond the two two neutrals together.
But in your situation where you are switching a load feeder or branch circuit only, you have no choice but the switch the neutrals too. As a practical matter, other than the potential hazard of a neutral in one panel remaining current carrying because it comes from another panel and circuit, the main show stopper would be if there were GFCIs involved.
But going simply by Code text, it is prohibited. Among the other prohibitions likely to be involved will be any applicable ones requiring all of the conductors supplying that load to be in one cable or raceway.
Note that if you switch the neutral in an MWBC, including a three-phase wye circuit, you may need to take special precautions not to create a momentary open neutral during the switching process. That can be a critical factor if you have sensitive electronic rather than resistive or motor loads on the switched circuit.