I don't know, but I'm going to guess "no" for two reasons. First of all, the rules say "an undeveloped small station hex" or a "small station tile", which seems to indicate the presence of only one small station. (I think if it were meant to include hexes/tiles with two small stations, it would have said so explicitly.) The second reason is that I don't really see how it would work practically. There are no tiles provided to indicate that you removed one of two small stations on a two-small-station hex, and so what sort of tile/upgrade would be appropriate?
I agree with Darin's analysis, but it would be nice to get official confirmation. Maybe the designer will comment.