George Nicholas specifies the charges against Gov. Jefferson

George Nicholas to TJ, July 31, 1781: “By the resolution of the House of Delegates an enquiry is to be made into the conduct of the executive for the last twelve months. No particular instance of misconduct was specified. They seemed to think and I am still of opinion that the persons entrusted with the administration ought to be ready to give an account of the whole and of every part of it.
  You consider me in a wrong point of view when you speak of me as an accuser. As a freeman and the representative of free Men I considered it as both my right and duty to call upon the executive to account for our numberless miscarriages and losses so far as they were concerned in or might have prevented them. In doing this I had no private pique to gratify….
  At your request I will mention such things as strike me at present as want[ing] explanation and if any thing shall hereafter occur I will inform you by letter.
  The total want of opposition to Arnold on his first expedition to Richmond.
  The dissolution of a considerable body of militia on our Southern frontier at the time of Green’s retreat for want of orders from the executive.
  The want of timely orders to the counties of Amherst Augusta &c. after the adjournment of the Assembly from Richmond.
  The great loss that the country has sustained in arms &c. exclusive of those destroyed by the enemy.
  The rejection of an offer made by Cols. Campbell Christian and McDowell to raise regiments for the Southern Service.” [PTJ 7:105-106]

Arnold's invasion of Virginia

During the first week of January, Benedict Arnold's troops headed up the James toward Richmond. On January 5, he ordered his troops to spread out to look like a large invasion force. The inhabitants scattered, and the unopposed redcoats captured the new capital (moved from Williamsburg to be safe from invasion at Jefferson's urging). The next day, General Nelson, commander of the militia, launched a counterattack, but it was thwarted by torrential rains that nearly drowned his troops and rendered his guns and ammunition useless. 

After the British moved on from Richmond, Major Richard Claiborne, the deputy quartermaster general, reported: “There is no commander here, nor will anybody be commanded. This leaves what public stores a few of the virtuous inhabitants have collected, exposed to every passenger, and the property of the individuals to the ravages of the Negroes. Both public and private property have been discovered to a considerably quantity, that was secreted clandestinely in and about town; and I am sorry to say that there is a stigma which rests upon the conduct of some of our own men with respect to the pillaging of public and private goods, that does not upon the British troops.”

Jefferson himself came under withering criticism for his unpreparedness and inattentiveness. It was not until January 19 that he convened the Governor's Council, and four days later that he called for the Assembly to convene. For weeks, he issued orders--more like suggestions--calling for the establishment of a battery at Hood's Point, a vital bottleneck on the James that would impede Arnold's ships if fortified. But nothing happened, and the incredulous British were able to pass through at will. Fortunately, however, they were in no rush to reduce the state, and redeployed to Portsmouth to spend the winter.

While the British fortified  Portsmouth, Jefferson had more time to devote to M. Marbois’ Queries. The Frenchman wrote him on February 5 to thank him for undertaking the project. “Hitherto it has been in my power to collect a few materials only," Jefferson apologized on March 4, explaining with supreme understatement that "my present occupations disable me from completing” it. Soon, however, he would “be in a condition which will leave me quite at leisure to take them up,” i.e., when he relinquished the governorship in June.

The lull in the invasion was only temporary, however.  On April 18, Major General William Phillips sailed past Newport News toward Richmond. Exactly a week later, Cornwallis's army crossed into Virginia from the South, and the two forces converged at Petersburg on May 20. Once again, the Virginia Assembly was routed from the capital, intending to reconvene at Charlottesville; but Col. Banastre Tarleton continued in pursuit, taking seven lingering Assembly members prisoner and laying waste Jefferson’s plantation at Elk Hill before sending an officer to Monticello to attempt to seize the governor himself. Warned in the nick of time, Jefferson rode off from his mountaintop home through the back roads to reunite with his family at his property at Poplar Forest some sixty miles to the southwest.