Stover, 61, had been free while his appeal was heard but is now in the Federal Correctional Institution at Ashland, Ky.
Meanwhile, a former president at another Massey coal company is also cooperating with prosecutors in the UBB investigation.
Former White Buck Coal Co. President David C. Hughart is set to enter a plea to two federal conspiracy charges on Jan. 16, the day before May's sentencing.
Hughart is accused of working with unnamed co-conspirators to ensure miners at White Buck and other, unidentified Massey-owned operations, got advance warning about surprise federal inspections many times between 2000 and March 2010.
They say that gave workers time to conceal life-threatening violations that could have led to citations and shutdowns.
Hughart's cooperation is a sign that authorities may be gathering evidence to target officials further up the Massey hierarchy. Some victims' families hold former CEO Don Blankenship personally responsible, though prosecutors have declined to say who else could face charges in the wide-ranging and continuing probe.