what every artist wants:
layer 1
layer 2
layer 3
what every software gives:
layer 1
layer 1 copy
layer 1 copy copy
what every artist wants:
layer 1
layer 2
layer 3
what every software gives:
layer 1
layer 1 copy
layer 1 copy copy
Blender does the first one (the right way) but with their File->Save As option.