Mine manager Warwick Lidbury will be performing the duties of acting CEO.
The court also ordered Mr and Mrs Jagatramka to pay the company's costs of the proceedings.
The selected mining section for the coal seams were revised based on economic criteria.
Additional work has now been completed for the Mod 4 application that was started in 2012.
The application was made after Russell Vale colliery was placed in care and maintenance.
It follows the NSW Supreme Court approving the schemes between the companies on February 14.
Work has continued to address the surface and underground mine assets.
The debt restructuring remains incomplete and various other conditions need to be satisfied.
Planning had started for the preparation of a modification application to extend Wongawilli.
The negotiations centre around two debt facility agreements.
Planning has also started to prepare a modification application to extend the Wongawilli mains.
The mine operator was directed to shut the conveyors down until corrective actions are completed.