I was using WithThreeJS to make my project, but ever since gdevelop arrived with 3D, my scene is just black.

If you build and run from the command line you can debug whatever is causing the JSON not to load.

WithThreeJS is not compatible with the built in 3d features for gdevelop at the moment. You should be able to get your project to display properly if you manually switch the layer property for all of your layers to 2d only.

FWIW, Pandako said he was working on making the next version of the extension compatible with the built in 3d features as well.