According to the FBI arrest affidavit, only six people printed that document, and she emailed The Intercept from her own work computer.
So she would have been identified even if she or The Intercept had the sense to remove or alter the DocuColor dots.
"The U.S. Government Agency conducted an internal audit to determine who accessed the intelligence reporting since its publication. The U.S. Government Agency determined that six individuals printed this reporting. WINNER was one of these six individuals. A further audit of the six individuals' desk computers revealed that WINNER had e-mail contact with the News Outlet. The audit did not reveal that any of the other individuals had e-mail contact with the News Outlet"
So she would have been identified even if she or The Intercept had the sense to remove or alter the DocuColor dots.
"The U.S. Government Agency conducted an internal audit to determine who accessed the intelligence reporting since its publication. The U.S. Government Agency determined that six individuals printed this reporting. WINNER was one of these six individuals. A further audit of the six individuals' desk computers revealed that WINNER had e-mail contact with the News Outlet. The audit did not reveal that any of the other individuals had e-mail contact with the News Outlet"