depends on where the spot is and how big it is, but in general I wouldn't worry -- all lens coatings do is allow more light to be transmitted by cutting down surface reflection -- sounds as if you'll have one spot on the lens where not quite as much light will get through, but it won't be enough to impact exposure or image quality.

when the lens gets back, use it and don't sweat it. My brother once showed me "the sharpest lens I own," a nikon wide-angle of some sort which had a rear element with a huge gash through the middle.

It's the light that gets through, not the light that doesn't, that makes the image.