I think this is probably OK, the house (new) has been approved for occupancy, but I ain’t a structural guy. Seems the WC had to go right over top of an engineered I joist, which required chopping through the I joist web. Two short sections of I joist were placed in front and back of the cut out section @ 90 degrees connecting the joist to the one behind it, there is also a 2X6 doing something it goes to the top of the next I joist.
I’m not a structural guy either. I can’t see the photo but it sounds like you’re saying they cut through the top of the I joist. I would have to recommend further evaluation at that point.
If they only cut the web of the joist and not the top or bottom chord then you need to refer to the I-Joist MFR’s allowable hole sizes and location in the web. Usually the further away from the bearing you are, the bigger the hole you can cut in the web. (I worked for Trus Joist for 20 years)
No good refer for repair. Ish
The flange was cut through, what I meant to say originally, the upper 2 by whatever, the toilet flange is dead center in the middle of the joist.
Can’t cut top or bottom cord without engineers work around. Refer it out, IMO.