Hmm... There is a possibility that the version of nwjs you are using may have a bug where it will crash the game when it tries to load the compiled js files. I had this issue as well in some versions due to breaking changes to V8. If you can, I'd advise updating on a newer version of nwjs. If you can't at all, then you can try including the --no-flush-bytecode argument in the package.json file for your game. This should fix that issue.
If it doesn't, let me know.
Also, as far as I'm aware, you can't mix files that are compiled with a different SDK. If you want to support 64-bit systems alongside the 32-bit systems, then compile the files separately for each version. Once with the 32-bit version of the SDK and the other with the 64-bit version That's the only detail that I can think of, aside from that your game can access a lot more memory in 64-bit machines.