I was thinking I would do exactly the same thing. I took all my covers apart and I was going to save the vinyl and the zippers for re-use, but I ended up finding mildew in about half of them.
I decided to buy new vinyl. The time and $ involved in the rest of the cushion cover construction and fabric just wasn't worth risking getting everything all mildewy again. Sorry, I'm not sure the reason for the vinyl, I thought maybe so that the cushions don't slide around on the
fiberglass, but I'm just guessing. (The old vinyl made a great template for the new covers though! It was also cheaper to buy the vinyl than the upholstery fabric, which works fine for me as you don't really see it much anyway.)