From what I hear, they did. I read an article early today that said the employees would be allowed to keep the overage.
I don't remember where I read that article, but I had to laugh, because the first three comments below it were:

I don't remember where I read that article, but I had to laugh, because the first three comments below it were:
- They should've told the people to keep the money in the first place.
- No, Microsoft shouldn't have even gotten themselves into that situation at all.
- Gee, it sure would be nice if there were, you know, some sort of spreadsheet application that could prevent this kind of thing from happening.