What should I do with shares I bought in a company, which I later discovered invests its money in usurious banks, after I had thought it did not deal in unlawful matters?

You are obligated to sell your shares in prohibited companies. There is no sin upon you for not knowing they were prohibited, and you are not required to purify the wealth earned from them. You may wait to sell them if selling them now would cause a loss, until you recover your capital.