So i am guessing you have your various files set out (config etc) and one central bot.js file, and you load the bot by using something like
node bot.js
on your host machine, and obviously part of your .js file sets up the bot something like this:
const bot = new Discord.Client();
From what I can tell, your
bot.destroy()
and
bot.login(botsettings.token);
is just refreshing the const 'bot', but what it is not doing is reloading your bot.js file (with the updated commands and code).
What you would need to do, is have it set up to run a batch file or something on your host machine that terminates the entire process bot.js, and then restarts it. As this would then use the new and updated bot.js file.
The only problem is I am still figuring out how to run a batch file from my JS file, as understandably for security that feature isn't built in (other wise most websites that use JS would be vunerable to getting it to run things like format C:\)
I imagine it will involve using WSH in my JS, and I will update here if I do get it going.
I hope this was clear? let me know if you still have a question :)