Doug:
Winnebago has complete wiring and plumbing schematics on their website (
Manuals & Diagrams). I looked at a Body 12V wiring diagram for a P36GD (you didn't say exactly which model you have) and found the Bypass switch turns on a "Water Heater bypass" valve and the Winterization switch turns on a Winterization valve.
The plumbing diagram shows that the Water heater bypass valve does what you would expect, i.e. disconnect the water heater and connect hot and cold together so you don't have to use 10+ gal of "pink stuff" to winterize the water lines.
I don't understand why switching the bypass switch would silence the alarm you were getting.
I can't figure out what the Winterization valve does, maybe it allows the pump to suck the "pink stuff" from a hose somewhere and fill the lines. Hopefully an owner who has a similar system will tell you.
Good Luck!
Stewart