I have the same issue, when I choose to view medium icons it show the default Unreal icon but another size shows my game icon.
“When I open my program exe (WindowsNoEditor\ITA\Binaries\Win64\ITA-Win64-Shipping.exe) using visual , there are two icon files attached. One has just my 256x256x32 bit png icon in it (correct). The other has a composite icon with not only mine, but also the default Unreal icons at 24x24, 32x32, 40x40, 48x48, 64x64, and 256x256. Depending on if I set the view in windows to be Extra Large, Large, Medium, or small icons I get either mine or unreal’s icon. This is despite the fact that the icon file I specified in my project settings has my icon at all those sizes. The build process is apparently copying the 256x256 version of mine icon into the unreal default icon file, but ignoring all the other sizes.”