Afternoon Dick,
Loads of this type of thing a few years ago, assuming that you used the scraper correctly, you should not have scratched the glass unless it was very old, any work like this is fraught with danger, so you should charge for this always,you should also inspect each panel carefully, before using the scraper and point out any blemishes, and get the client to sign these off.
No matter what you do in this instance, I think your customer will always think that you are responsible, personally I would replace the scratched panel foc as soon as possible, but ensure client knows that she is important to you and your business and you are doing this as a goodwill gesture, and are not accepting any liiability.
Regards,
Rob