They do overwrite and that's intentional. It avoids bugs like "deleting ability crashes editor", for instance. I do all the ability modification outside editor.
Attached are all the files required(I hope) and a map that uses them so you'd have a working example to look at. You'll have to copy the contents of the lua folder into the lua folder of your JNGP(it requires JNGP to work).
Pay special attention to the "Objects" trigger in the initialization - this is the lua code that runs the whole object generation thing. The "addEngineers" function from HeroicFunctions is a function that I made specifically for this map and it's not needed, but if you understand some lua it can show you how to use the system even better.
You can test whether you've saved the map correctly by just saving it. I just tested that it gives me no errors, so if it does give errors for you it's a sign that something has been set up wrong.
The objects are generated on every save, as long as the lua script hasn't been commented out.
This is not an official resources, so I don't want to support it. If you need help you can ask, but I won't fix anything that requires effort.