For linux I had to end up pointing to the icon in my main root directory of my project.
"linux": {
"category": "Utility.Passwords",
"icon": "CYaPass.png",
"executableName": "cyapass"
},
"win": {
"icon": "build/CYaPass512.png"
}
You can see that I pointed to the one in the build directory for my windows icon and it worked.
I remember having challenges with this myself but it finally worked when I did it this way.