Hello John! This definitely should not be the case, and I haven’t heard of anything like this happening. Can you give it another shot? Make sure that you know exactly where the file is being saved… Then reload?
Keep in mind that when you start a new file, there aren’t any layers in it. When you click the DESIGN button, or run any ConDoc Tool, then you will see the layers appear from your drawing set.
Let me know if you get to the bottom of it!