Is it permissible to take a share from the proceeds of selling the department's books, knowing that these proceeds include a portion from the sale of a stolen book, and does this make the money unlawful (haram) or subject to the doubt of unlawfulness (shubhat al-haram)?

The money earned from selling stolen academic material is not entirely unlawful (haram). Only the proceeds from selling the stolen book are unlawful. Therefore, these proceeds must be identified and disposed of by spending them on the general welfare of Muslims. If you cannot identify the exact amount, act based on your best judgment. The person who sold the stolen work should be advised that its price is not permissible for him.