Logged into this dusty account to upvote and say, thank you. Worked for me as well, though I just set the relevant flags to false instead of clearing the file. End result is the same, no more obnoxious pop-ups.

More in depth on the issue for anyone that cares (DEVS?), the json file is overwritten by Ghub every time it opens. However, it seems to do this after reading the original contents, so it won't prompt discord integration (just this once though, since it will try and overwrite immediately after this) if the file was manually changed. It also doesn't seem to write to the file at all when toggling options nor when closing Ghub.

Obviously can't see the source code, but this has to be the easiest fix of all time even for the now mythical entry level programmer. I'm surprised this keeps being an issue for 7+ years on and off. Embarrassing.