Question about phasing in Bard wall unit

Hey guys, I find myself in an odd situation. I landed a new job and I’m the sort of the lead guy in hvac troubleshooting even though I have zero experience in central air systems. We have 100’s of units so I’m learning rapidly but this has me stumped.

I came across a Bard wall unit yesterday that wasn’t running. Somebody was in there messing with it at some point and apparently blew up the original transformer and replaced it. They also removed the jumper on the low voltage board that went from W1 to W2.

First thing I did was replace the jumper. The phase monitor was also showing it was out of phase so I tracked the wire feeding it through the control module and all the way back to the transformer.

I removed the 120v feeding the transformer from the contacter and somehow the line side wire of the transformer was still showing 120v and that tells me the transformer was being backfed from somewhere.

It actually worked out perfectly because I was able to check the phases across to the contacter with a fluke and quickly determined which phase was the right one.

I de-energized the circuit then swapped the two wires on the line side of the breaker and it worked immediately.

So my question is, since the 24v transformer was apparently being backfed, where was the 24v that was backfeeding it coming from ? I scoured the schematic and the unit and I’m certain there’s no other transformers in the unit.

There was an identical unit that was running in the same building and each had its own thermostat. The wiring went up into a giant cable chase so I couldn’t tell if the two thermostats were connected without taking them apart but if they were connected and the phases were off wouldn’t the other unit show it was out of phase too ?

These units cool a bunch of electrical distribution equipment and we were in a heat wave so I didn’t want to risk opening up anything else.