Same issue. It seems that encrypting the files will cause the main.js to be impossible to locate. It's a pity if we can't use encryption and source code protection.
Not sure if it is the same issue as Daisuke's but it's quite weird that a JS file is missing.
If you can, please provide the logs for the app. You can get them via Utilities -> Extract logs.
A bit of an update: R6.02u6 has some re-work for hotpatching, which may address the issue that you are encountering.
