Fuel Injector up-sizing calculations

When up-sizing a fuel injector size. What's the best way to tune a fuel table to suit that is in injector pulse width?

I'm thinking that I should calculate standard injector flow then update field with required pulse width to achieve the same flow with the upgraded injectors. Eg. 500 cc inj @ 3ms would be the same as 1000cc inj @ 1.5ms, Is this correct?

Your logic is correct and this is the way I'd make a broad sweeping adjustment to get in the ball park. Take the new injector size, divide it by the old injector size and then multiply the entire fuel table by this factor. You'll obviously need to update the dead times to suit the new injectors too.

This likely won't be perfect though as the Haltech ECU doesn't account for the non-linear area of flow and it's pretty likely you'll have some differences here. You'll find there will still be a small amount of work to do to get your AFR back on track but you should be very close.