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In its final week in office, the Bush administration might have some serious work to do: recovering millions of emails. For over a year, the administration has battled a lawsuit by two Washington-based watchdog groups seeking to force the White House to locate unaccounted for internal emails, and on Wednesday morning a federal judge issued a last minute preservation order [PDF].

In full, it reads:

The Executive Office of the President (“EOP”) shall: (1) search the workstations, and any .PST files located therein, of any individuals who were employed between March 2003 and October 2005, and to collect and preserve all e-mails sent or received between March 2003 and October 2005 and (2) issue a preservation notice to its employees directing them to surrender any media in their possession–irrespective of the intent with which it was created–that may contain e-mails sent or received between March 2003 and October 2005, and for EOP to collect and preserve all such media.

This is a major assignment for the Bush administration, which has to date been tight-lipped about what it has or has not been doing to preserve its emails for post-administration archiving. “The EOP [Executive Office of the President] is going to have to go to each of the workstations and find PST files and save them,” says Meredith Fuchs, one of the lawyers representing the National Security Archive in the case. “It also means all of the EOP employees who may have used CDs, DVDs, external hard drives, zip drives, memory sticks, etcetera, to save emails are going to now have to turn them over before they leave.”

It’s unclear how much of this work, if any, the Bush White House has already completed. But it could potentially throw a wrinkle into what has so far been a smooth transition: “It’s going to mean they’re going to have to work a little harder as they walk out the door,” says Fuchs.

The judge’s order doesn’t place a deadline on the White House, but since the National Archives is days away from taking custody of the Bush administration’s records, Fuchs believes the ruling must be satisfied before Bush departs for Texas.

A status hearing in the case is scheduled for Wednesday afternoon, and it’s possible the administration’s lawyers could seek to change of the terms of the ruling. At the very least, says Fuchs, the order “requires them to come forward and say what they’ve done” to preserve and recover any missing White House emails.

Whatever the outcome of Wednesday’s hearing (more on that later), the missing emails controversy seems destined to carry over into Obama’s presidency—and it remains to be seen how his administration will handle any ongoing litigation. In a related matter, which could be read as a positive sign for government accountability advocates, Obama has pledged to “nullify the Bush attempts to make the timely release of presidential records more difficult.” This suggests that his administration may seek to overturn a Bush executive order giving current and past presidents, along with their heirs, greater control over the release of White House records. But with the economic stimulus package, along with other pressing issues, on his plate, restoring the Presidential Records Act and dealing with any lingering White House email issues may not figure high on his to-do list. Says an Obama transition aide, “We are in the process of working through these issues, but the commitments that President-elect Obama made during the campaign will guide our decisions moving forward.”