Follow-up to #668. Unity's ModelImporter replaces UV2 when "Generate Lightmap UVs" is selected in the importer, UnityGLTF currently just uses the underlying Unwrapping.GenerateSecondaryUVSet() method, ...
Use the Lightmap UVs action to manually generate any missing lightmap UVs. This works on each Mesh in every open scene that is missing lightmap UVs.