These are the steps I took to change a modest project from CoffeeScript to ES6.
My ~2000LoC project took me around 6 hours to port, but I sunk 3 hours into a stupid mistake, and 2 into figuring out these steps, so with these steps & warnings at your disposal already, you should be able to do bigger projects in considerably less time.
Automatic tools only take you so far, there will be some manual fixing. Sometimes the generated code clearly doesn't look like a human wrote it, and sometimes there are bugs.
In this last case, when porting software trips over a particular bit of CoffeeScript, comment this bit out, and try transpiling the file again. If this is successfull, you'll see the commented CoffeeScript inside the JS, and you can port that bit yourself.
Okay let's dive right in!