Don't worry! It happens to the best of us! But luckily for you, here is this nifty tool to help you out.
Great Question! Its simple! Just open the jar, and either click load and select a file, or drag and drop one in. Then, click any of the buttons to mess around with the layers. The 'cycle' button moves layer 1 to layer 2, layer 2 to layer 3, and layer 3 to layer 1. The other buttons are self explanitory. You can click these as many times as you need, for example, if your layer 1 is what you wanted to be layer 3, you can click the cycle buton twice. There are also three tickboxes wherein if you only have your geometry wrong, you can uncheck tiles and prop depth to just swap the geometry. Etc. Now when you do this, it'll change the layers in memory meaning nothing actually happens until you click save. When you click save, it will automatically save a file in the same location as the one loaded in, only with _widtotwl appended. However, if you shift click on the save button, you can manually choose a save location.
Okay! Dm me on discord, @LudoCrypt and I'll answer anything you may have.
Okay! Either dm me on discord (see above) or open an issue report.