From what I gather you're referring to what's known as the pinch weld.
I.E. The flange that the rubber seal lips over to retain the windshield.
Just be careful to replicate the correct size as if it's too large,the windshield fit will be too tight.(How much do you have to replace) any pics?
If you're welding,skip around to avoid excessive heat build up.
Make sure you make the area smooth to allow the gasket/seal to work correctly.
