I would suggest, just emailing the customer and advising them that only part of their order is available (if your website does not tell them) and seeing if they want to have it shipped as two shipments (and occuring two shipping charges) or if they wanted to wait for fabric A and hope that is it available when fabric B comes in.
Sometimes people are buying things to go together and wouldn't want them unless they had them together. I think as long and you communicate honestly with your customers they will understand.