Sorry for the delayed and short answer.
In this case it would really be the best to rebuild the engine and SDK from scratch, if it’s about the GLTF Converter in the SDK.
The engine comes bundled as nbm, but once you build a nbm, you can build them all. Patching just the jar may fail due to checksums or whatever else there is.
Maybe you can also write a simple script in a language of your choice to just strip that extension off.
Ultimatively, it may be worth to raise an issue on the engine github, so we can properly fix that, but that change will take time to propagate. Another thing here is the header of the file, gltf as extensionsUsed and extensionsRequired (or something) and for the latter, failing is no bug but a feature.