I realize we are talking about a mile under the sea, but I do not understand why capping this sucker is so difficult. I wish there was somebody who would answer what appear to be the obvious questions from a plumbing/engineering perspective...
I can't find any stills or at least as easily as video, so take a look at this.
Why they tried to use ROV mounted circular saws and then eventually used the shears to cut the pipe baffles me. A chain cutter or similar is what I thought was the preferred method for cutting large diameter pipe, or some device that clamps to the pipe and then circles it with some sort of cutter. With a clean cut, you could thread the pipe maybe, design a seal for it, or whatever. They just replaced a reduced flow kinked piece of pipe with a tweaked higher flowing one.
Why they just don't unbolt that flange and bolt a valve, new BOP or whatever on top of it.
Or if you can't unbolt it, at least it is a known diameter and solid, so design something to seal to it and clamps below it.