The code does not address your question.
If you have a problem with flange alignment it is sometimes better to cut the whole flange off and start again - much easier to clean/prep for the new weld.
You can do what you have suggested but it makes it much harder to have good preparation for welding.
That is why welds are nominated as FFW (field fit welds) so alignment is possible with already installed flanges.
Cheers,
Shane