Is notching a flange on an I-Joist ever acceptable?
According to this document (PDF), accidental notches in the top flange may not need to be repaired if they meet specific criteria. To determine if a repair is required, we'd need a bit more information, including:

The distance from the center of the notch to the end of the beam.
The depth of the notch.
The specific beam used, including beam height.

If a repair is required, it may be as simple as gluing and nailing on a 2x4 and some backing material.



This repair can be placed on either side of the beam, so in your case, it could be done on the side opposite the pipe.
Note that the building code specifically says &quot;unless the effects of such penetrations are specifically considered in the design of the member&quot;. This means that the manufacturer of the beam is the one that determines what type and how much damage requires repair.

IRC R502.8.2 Engineered wood products.
Cuts, notches and holes bored in trusses, laminated veneer lumber, gluelaminated members or I-joists are not permitted unless the effects of such penetrations are specifically considered in the design of the member.

If you don't trust the advice of your builder, or simply want a second opinion, you could contact the local building department, and see if they'll come take a look. Contacting a structural engineer is another option, though I'm sure you'll have to pay them for their time.
While damage to these types of beams is concerning, it's better to seek professional assistance, rather than relying on the lunatic rantings of a bunch of dimwits on the internet. Now that you're done reading the lunatic rantings of this dimwit, seek the advice of somebody with a framed piece of paper on their wall.