The Washington Post had a lengthy and informative article on the matter. Part of that article states "Archives officials, after a year-long investigation, say Lowry signed a written confession Jan. 12 that he brought a fountain pen into the research room sometime in 1998 and wrote a 5 over the 4 in 1864, using a fade-proof ink. Lowry, a retired psychiatrist who discovered the pardon in an unsorted file box, has denied any wrongdoing. He said he was pressured by federal agents to confess."
Never, never, never alter an original document, never "correct" items that appear out of order, don't reorganize files, and shudder, never take any document. If something in a file or box at any repository seems out of order or that something is awry, bring it to the attention of the staff. Like with the airlines, even careful and innocent people will be subjected to greater scrutiny because of the misdeeds of a few