Hey everyone,
unfortunately, the menu item Select → Deselect Layers does in fact not deselect Layers inherited from Designer (and probably Publisher, haven't tested) documents. (E.g. opened a logo constructed in Designer for further post-processing-effects via File → Edit in Photo).
Attached is a short demo, recorded with Photo V2.1.0.
Cheers
Dennis
Deselect_Layers_Bug.mp4