I believe the bug here is that the deleted layer style should be deleted from all comps. Deleting a layer style should be treated the same as deleting a layer. Layer comps can't store a different file structure, just different settings. The workaround, or the correct way, to have layer styles visible in one comp and not another is to turn off the layer style visibility. Then it will work correctly. I'll log a bug for Tim to take a look at.