Must the suspicious money be repaid to the employer again, whether it was disposed of in charitable ways before knowing the Sharia ruling or after?

Funds unlawfully taken from government entities must be returned to those very entities, unless this is impossible or would lead to significant harm. In such cases, the funds should be spent on charitable causes and for the benefit of Muslims. As long as you are able to return the funds to the government entities, your obligation is not discharged by giving them as charity; rather, they must be returned to the entities, except in exceptional circumstances.