The decision to cut about 300 medical center payroll jobs and move about 300 more are part of broader efforts to reduce the size of the VA workforce.
Software handling timecards for VA employees has been malfunctioning for nearly a week, prompting concerns about paycheck delays.
Thousands of federal employees could be reinstated to their government jobs following the ruling.
An internal memo instructs top-level Veterans Affairs staff to prepare for an agency-wide reorganization in August.
