First, validity of a marriage can be challenged at any point. And it generally isn't considered fully checked at time of marriage - marriages where "proper" documentation were presented can and are challenged, sometimes with the marriage being declared void.
There is also no general statute definition of man or woman. So when they wrote "one man, one woman" into the law, they didn't define man or woman. So it's up to the interpretation of the courts. Your marriage in VA will be considered valid after your spouse's SRS if challenged only if a judge believes (A) it's constitutionally required to allow same-sex *OR* (B) if the judge believes gender is fixed from birth and thus your spouse is an opposite sex partner.
That said, most marriages would never be challenged. Before DOMA and the state-by-state amendments, there would be little question that the marriage would be valid if it was valid when entered into. But today, that's not certain. That said, I'm unaware of any marriage having been declared void after one partner has SRS.
For things like federal taxes and such, it's uncertain (the IRS does have access to gender information from social security).
It's this ambiguity. Different states can see it differently, and that's not right. That's what motivated me to support same sex marriage. Right now, T people are just collateral damage while the right wing goes after LGB's.
If you are highly concerned, I'd suggest talking to a lawyer. That said, unless the law is settled in VA (I doubt it is), even a lawyer likely won't know. For me, I'm in a heterosexual relationship that some states won't recognize. I don't know if the feds would recognize it or not if it were to get contested in federal court. But I know being married is right, and am willing to risk legal consequences. Different people may make different decisions.
