The rebates are instant rebates, which means they are applied at the time you pay. To get the rebate you must buy the lens within the rebate period. Some retailers will charge your card now (thus allowing you to get the rebate credit), even if the lens is not in stock. If you buy from someone that charges your card only when they ship, it is possible that the rebate will not be applied. However, as long as you buy it within the rebate period, I'm sure most retailers will honor the rebate credit, if the lens ships after the rebate period.
Just curious what lens are you wanting that is out of stock?