Wiring Emergency Stop button to disconnect two independent circuits
If I understand you right, this is your circuit diagram:







simulate this circuit &ndash; Schematic created using CircuitLab

I can see at least one problem here: 
If the ESTOP is in open position, there is still a closed circuit GND-&gt;BAT2-&gt;RLY_2-&gt;RLY_1-&gt;BAT1-&gt;GND. Which is not a problem when BAT1 and BAT2 are EXACTLY same voltage, and canceling each other. But in the world of batteries it is not the case. They can be charged to different levels, or there can be voltage drops due to current spikes (especially with motor applications), so there will be always current in this circuit, which might be enough to close the relays whenever not intended.