What I would do, once you have the layers apart sufficiently, is lay a new strip of batting underneath the existing batting, overlapping about 6 inches. (Make *sure* the backing fabric is pinned out of the way!!!). Cut through both layers with a rotary cutter, making curves. Discard the narrow strips. The remaining batting will "nestle" together.
You can machine zigzag these two pieces of batting together using a very wide zigzag that is fairly far apart -- just enough to hold the two pieces snug against each other. Using this method, the batting pieces do not overlap each other; the zigzag stitch holds the join.
The curves make sure that the join doesn't show later on.