Hi,
this might not be an LWJGL issue or bug, but generally Assimp related. I spent now a lot of time trying to import and export animated models and animations with Assimp, unsuccessfully. This post can serve as a kind of a warning to other people if they try to use Assimp for exporting models.
Animations are not implemented in the Assimp FBX exporter. I looked at the Assimp github source, and this is missing, its not documented anywhere either. The armature can be exported with FBX and it imports ok into Blender, but not the animation. The Blender 2.79 FBX importer is not the best either, but it opens the model, with matching armature, but rotated bones. The FBX model (even just static model, no armature) exported from Assimp can't be opened in Maya or MAX, but Blender handles it.
The armature exported wtih Assimp Collada exporter imports wrong into Blender.
Exporting animation with Assimp crashes the JVM. Its a C++ exception, somewhere in the destructor of the AIScene class. So practically the whole export process completes, but crashes at releasing the scene.
The best result to export an armature to Blender with Assimp is by using GLTF2 exporter. The armature imports perfectly into Blender.
But trying to export the animation, even if empty, will either return with an error code, or crash the JVM, in the destructor of AIScene. Sometimes the file with animation is written, but it is wrong in Blender.
So in the end i had to resolve to my own PSK/PSA exporter/importer to get animated models and animations into Blender and from Blender. There is a patched Blender PSK/PSA importer source available from GitHub, and its possible to write a matching exporter for that in Java.
Its a petty that Assimp supports so many formats, but can't export animations with either of the formats.
I see two possibilities to have animated model import/export based on a modern format:
1. Make a direct wrapper for the FBX SDK. Only the FBX SDK can read/write FBX files perfectly. Blender can read/write FBX files not perfect but good enough, so this could work, when Blender-specific stuff/bugs are also considered. The drawback here that its another binary library, so if there is some error, it will crash the JVM. Its a black box just as Assimp is.
2. Make a GLTF2 exporter/importer in Java. The format is pretty readable and open, much simpler than FBX in structure. The existing Java GLTF2 importer/exporter does not look optimal, but would be a good starting point. Its still a question if the Blender GLTF2 animation importer is usable enough.
All in all, the animated model import/export situation does not look too good around Java.