de facto officer doctrine will not apply to Obama, he was challenged on eligibility before he became President and those challenges continue. He and the Nation were put on notice and failed to remedy the situation. It is also not just an administrative issue,
Let's suppose that a court rules that Obama is ineligible for office, and that this then goes to the Supreme Court, which agrees with the decision. Is the Supreme Court then going to strike down every law and executive order signed by Obama because Joe Blow questioned his right to hold office in 2008? No, they are going to say that Joe Blow is out of luck because he couldn't convince enough people before the election. This is exactly where the de facto officer doctrine will apply:
"The de facto doctrine springs from the fear of the chaos that would result from multiple and repetitious suits challenging every action taken by every official whose claim to office could be open to question, and seeks to protect the public by insuring the orderly functioning of the government despite technical defects in title to office."
The only exception will be if Joe Blow was involved in a court case regarding a decision made by Obama, the case was filed around the time of the decision, and Joe Blow challenged Obama's legitimacy during the case. If the case went against Joe Blow, he might later have grounds for appeal. But the court is not going to open the floodgates and let thousands of these suits cancel out laws that apply to everyone, when there is a legislative remedy.