No need for all the apologizing, it's ok. I do disagree tho, it is a big process of trial and error. There is a reason software like these are called "editors" not "creators" tbh.
The usual workflow, as you said, is to prototype first. You make a barebones version of everything you imagined and then you slowly develop all the things to a more and more finished state. But that means a lot of editing, not less editing.
As for skymen's take, I just think an engine's interface is all about you not having to do everything from scratch in a text editor.
Mistakes happen, but all the trial and error should happen in prototyping phase, but you moved into production when you created many levels that you now have to change. In the production phase, all you should really be doing is reproducing your successes.
It's a little like putting the cart before the horse, but you want the cart manufacturer to build you a crane so you can more easily move horses around, because in the back of your mind, you know you'll probably put the horse in the wrong spot again. I'm just suggesting to put the horses first so you won't need a crane.
You work however you want to work though and do what's best for you. You like the entire process to be trial and error, that's fine. I was only making a suggestion in case you were unaware of am more established way of working. I'll stop wasting your time and let you all get back to brainstorming solutions. I wish you success with your app and getting this new feature added to the editor!