I have created a layer from an existing layer using the select by location tool. I then saved this layer and removed my main layer from the map. I had to trim up the new layer to fit my project. When I add back in the original layer to overlay the new layer and show the changes the original layer has been deleted in the same places as the new separate layer. I have tried this process several times and always get the same result of the original layer being deleted in the same places as the newly created layer.