The following part is made for double-shot injection. The shell should be consist of two equal-thickness layers, each made with different materials.
Thus I want to create a multi-body part where each shell layer is a single body.
I tried to apply "Shell" feature twice. The first time it creates the outer layer. However, the second time the "Shell" feature moves the outer surface of the outer layer inwards and become the inner surface of the inner layer, and the outer shell is not preserved. You can see this effect by rolling back and forth between the "Outer Shell" and "Inner Shell" operations.
What I want is to create the inner shell as a separate body while preserving the outer layer as another body so that they are placed together in one file.
Your corner fillets are causing problems in the 2nd shell in image, but not in model you provided. Try this instead.
Either:
Perform one shell to the thicker depth (1.30mm).
Offset Surface (in Surfaces tools) of the outer faces inward halfway (0.65mm).
Use the Offset Surface as a cutting tool to perform Split command, cutting two bodies and keeping both.
Now it has two solid bodies. I think that's what you wanted. See FM in image.
I'd attach a file back, but it went and poisoned your work with my part templates in the Split command, resulting in mixed units, I'm sure.