There is no way that your phone wouldn't get the update because you had a certain file on your SD card. Your system knows what version it is, if the system wasn't updated, having update.zip isn't going trick anything into thinking it has. Of couorse, if you have it rooted, or changed the radio version, or anything like that, it may have prevented you from getting the Over The Air update, but I don't know all of the factors for your specific phone.
But specifically, no, I seriously doubt having update.zip on your SD card would have made your phone ignore the official update.