Lol seeing all your edits reminded me of what I went through. It's such a headache to test isn't it?
You're right about the debugger - this whole issue relates to popup windows, but sometimes I've used C3 in NWJS for long periods of time, and I preview in popup windows, and I always use popup windows to drag onto a dual-monitor, so all is well and stable for hours... Until I use the debugger and it just nukes C3 and you have to delete appdata yet again, login, install plugins, set your c3 settings again, change your theme (which requires restarting C3), etc. And then you find that when setting everything up, it might corrupt your appdata AGAIN, so you end up running in circles, deleting appdata again, login, avoid something like installing plugins, set your c3 settings, preview a blank project, then it may/may not corrupt your appdata folder again...
My suggestion to you: I hated the risk of losing unsaved work, so I've now moved to using C3 in Chrome, but using the Remote Preview Tool to preview in NWJS. All you do is use remote preview in C3, copy the URL, open the Remote Preview Tool, paste the URL into this tool, and voila, you're testing in NWJS as simple as that. Each time I preview my project, I click "remote preview" and then I click "reload all" on the little remote preview popup in C3. Quite good!
However, one issue that I haven't found an answer to: I don't think you can use the debugger for remote previews, which is such a major loss, so currently I workaround this by having to use a spritefont that appends whatever info I want to debug. It's good enough, takes a bit more time though, but you can't use all the other useful features from the debugger, such as viewing the event sheet CPU usage.
Regarding C3 in NWJS, I've tested this on a fresh new VM with Windows 10, and the issue persists, so right now, I'd strongly urge everyone to avoid using C3 in NWJS, even from the official source or the third party launcher (which I always used and really adore!) but for now, you will run the risk of C3 suddenly closing with no error, possibly lose unsaved work, and then you need the computer knowledge to find your appdata folder and delete the right folder and waste time setting up C3 again, with the chance that you might need to repeat this process multiple times to get it working again.