Beware. Something similar to this happened with my old Passat. The humidity is very hard to get rid of entirely - even with very thorough vaccuming and baking soda. My flooding hapenned in the Fall, had no probs during Winter, and then -after weather picked up again- cabin had an omnipresent mild humid smell.
Treat the flooding with extreme care, make sure no moisture is trapped between the bodywork and carpeting.