A jackhammer and reshooting that section after the plumbing has been moved.
Honestly if it were me, I would leave them as is. With surface matched drain covers they will hardly be visible and tearing into your pool shell can create a whole new set of issues if not done correctly.
Another option, since it looks like the stub on the left is centered, is to cancel the right stub and use one of these instead:
More here, Posting Photo's Tutorial
I like Brian's idea, the dummy, or leave it. No one will care but you, and I promise it won't be that bad. I'd rather it be centered too, but I sincerely think it won't bother you with a little time. I wouldn't want to risk breaking up the shell if it were me. Maybe it wouldn't be that bad, but that would always be a worry in my mind. I hate having a nagging doubt that will sour the whole experience, and cutting the shell would put that in place for me. It can be done, but it will be no small task done right.