Dual Y End Stops

I have taken over using my companies X-Carve.
I am currently rebuilding it with a new spoil board, upgrading the spindle and applying the new X-Carve upgrades.

While going over everything I have noticed a flaw in the design, there is only 1x end stop for the Y-Axis even though there are 2x motors.

In the old system our Y-Gantry would become twisted if one motor skipped a step and became out of sink with the other. To reset the machine you have to turn everything off and manually set the second motor.

Is there a way to modify the new X-Controller to work with 2x Y-Axis end stops? So when it homes each motor is reset?

No. Even though it has separate motor drivers, they are slaved together and are not independent. What Robert said about the tensioning is the only way to ensure they stay the same. Others here have suggested a block to place between the ends and the axis to set the position evenly before powering up.