in my app the main.js of my electron application is in the toplevel application source folder (in /src, below the folder where the package.json for electron-builder is):

  "main": "main.js"

The packager considers to look it up in

../dist/"appname"-win32-x64/resources

Where it really is after packaging (asar is false):

../dist/"appname"-win32-x64/resources/app

if I change the entry in the package.json to

  "main": "app/main.js"

packaging is working, but that's not the relative location of the file.