Need more info. Did the 3-way switch, or wiring there of, have anything to do with the problem?
No. It was just the HO showing off his new fancy tester that he thought the red light meant that's where the problem is. The red light simply indicated the presence of voltage.
I would find out what was on the circuit that trips the main when the breaker for that circuit is turned on.
It was marked "Kitchen hall bath basement lights"
Unless the main isn't breaking contact on both legs, how is "half the house" going off?
"Half the house" going off is simply the HO being confused.