If experiencing export problems with files created with an earlier versions.
Check if the workbench preference : Export utilized Geant4 Materials : is set

Either : Unset the option.
Or create an up to date version of the Materials section by
- Opening a new file ( Creates all the GDML Groups)
- Select all the Objects under the WorldVOL in the old file
- Copy to WorldVOL in new file
- Check structure is the same.
- SaveAs a new version