I would say just bite the bullet and change over all the substrate. As chadman said, the sand will filter its way to the bottom of the cc. I had cc too and a few months ago I decided to change it and I haven't regretted it at all. I don't know what size tank you have, but it wasn't that big of a deal to do it for my 55 g.
I put all my LR in a bucket w/my cleanup crew and fish and filled the buckets up w/tank water. Then I got a large yougurt container to use as a scoop, had my roomate hold a garbage bag open and I went to town scooping it out. Then I placed the LR back in w/o any of the other critters and poured the LS in around it. The I put the fish and everything back it and there wasn't any problems.
It was a much simpler operation than most people make it out to be, but maybe that's just because I have a relatively small tank.
