as mentioned above you start to cook the battery. so you would eventually have to replace the battery due to damage.
as for the bypass, you shouldn't disconnect any wiring.
you are just adding a wire to the ballast.
you should find in the wiring diagram that the ballast shares power with the input to the vr. and one of the field wires to the alt.
the second field wire is what is controlled by the VR.
so when you add the bypass, it puts the sensing voltage from the ballast with battery voltage correcting your drops in voltage as it travelled.
so it is back feeding the vr with power you added to the ballast.
a more permenent solution is as I mentioned to use the sensing line to fire off a relay and then providing the vr/ballast with battery power directly through the relay. takes out all the connectors.
but you can clean it all up as well.