If a piece of transparency isn't matching up as it's suppose to, and repairing it risk messing up the entire project, or causing a pile of extra work, I will fabricate my OWN transparency's using the thin clear plastic tops from Greeting Card Boxes.
One can even use the "bad" piece as a vacuform mold for a *slightly larger* replacement part. While trimming the new part to it's regulation size, leave a couple excess pieces of the plastic, to make glue tabs, and avoid the danger of clouding altogether.
(plus, if you've already completed the finish and don't want to risk messing it up, this method works great!)
Frank