Flatten quilt can be inaccurate if you are unbending sheetmetal that is bent in 2 directions. Tho in your case better option would be to draw new pipe without cutouts then make sketched rip. Then make those cutouts. Or if its imported part copy surfaces of those cutouts into your new part with whole pipe and then use solidify to cut pipe as original.
I cant open educational version so if you can give us step/iges it would be helpfull.
