With new units under construction, isolated-phase bus ducts are being installed. These are aluminum, about 36" in diameter. One section was damaged in transit somehow and is about 1" out of round through about 5' of run. A rolled rib was deformed and broken through. Should there be concern about phase differential in this phase of the duct? The recommendation is to cut out the damage, restore the profile, weld it back in, and recoat the inside.

This is a question for the manufacturer, not for an arc flash forum.

Any customer modification or repairs in this case, to the bus will most likely void the mfg warrantee. If the bus is UL listed it will void the UL listing.

Welding alum is tricky. I would be concerned about stress cracking at the weld due expansion coeficient of alum due to ambent temperature changes especially under high amp loads. Welding alum also hardens the material. If it was me... I wouldn't use it unless the mfg agreed to the repairs, tested the bus after repairs and signed approval to installing it.

As jghrist said this is a question for the bus duct manufacturer.

Look at it this way, If you bought a new car, but what was delivered to you was a beater,( with a coat of bondo to take out the dings), would you be happy? Why should you be willing to take a less than brand new bus system? Either the shipper , or the mfg should be replacing it.