There are two different electric things going on. The light switch has the manual Low High CHARGE CONTROL, its used (as original) when you DO NOT have a full fledged Voltage Regulator (IE the old original cutout relay system). If you converted to a Voltage Regulator system, the light switch no longer regulates charge but ONLY the lights and its no longer wired down to the gennys FLD terminal.
The Cutout Relay has but two terminals, BAT and GEN, it connects the gennys ARM post to the battery (via ammeter and relay) when shes charging (cutout relay closed) but opens otherwise upon shutdown.
Sooooooooooo you can 1) Buy a new Cutout Relay and continue use of the light switches Low High charge control (it has a wire down to gennys FLD post) 2) Convert to a full fledged Voltage Regulator which as an internal cutout relay PLUS it wires to the gennys FLD to regulate charge and you no longer run the wire from FLD on genny to the light switch.
OLD Cutout Relay system: Gennys ARM to ARM/GEN on cutout relay and BAT on relay to ammeter,,,,,,,,,Gennys FLD to light switch
Voltage Regulator System: Gennys ARM to ARM on VR,,,,,,,,,,,Gennys FLD to FLD on VR,,,,,,,,,,BAT on VR to ammeter
Some just use a DIODE to replace the old Cutout Relay
Talk to Jim at Agri Services in New York www.wiringharnesses.com I think??
Id keep it original, just buy a new cutout relay and use the manual light switch Low High
John T