Is it possible to save a modified Java 3D scene graph back into a VRML .wrl file?

I am not aware of a Java 3D scene graph-to-VRML file exporter, though something should conceivably be possible to write (I think...not having done it yet myself). You should be able to get the information you need to at least write out a simple VRML wrl.

Background info: Sun has discussed providing a persistence mechanism and binary file format for Java 3D that would at least let one dump and restore scene graphs. Something like this is certainly needed.

For information on loading VRML files into Java 3D scene graphs, please refer to this related FAQ entry.