I did this the other day with cupcakes. I was making 2 batches - chocolate and banana. I somehow ended up with not much normal flour (only wholemeal) and not much white sugar (only brown). With the chocolate ones I made them wholemeal with brown sugar, with the banana ones i used as much white sugar and flour as I had. I figured chocolate would hide the fail more. They were both lovely.
so yeah, I wouldnt worry about it. Let us know how they go!