When you "merge visible" you need to deselect the layers you want to preserve by clicking on the eyeball icon on the layer. It should not merge any layers that have the eyeball removed.
If you are doing that; then I'm not sure what is going on.
You can always find your CM .ACV files under history. I use that feature all the time when I am editing images shot under the same lighting like a wedding or a portrait session where the lighting has not changed. If you need some screen shots let me know...
Greg