Is the money returned by the seller lawful for the thief if he purchased with stolen money, then later purchased with lawful money and the remainder was returned to him?

The sin of theft is tied to the thief's accountability, not to the stolen money itself. So, if the thief returns the equivalent of the stolen money—even if the stolen item itself is still with him—his accountability is cleared. The money of the shop owner does not become unlawful (haram (definition)) just because the stolen money was mixed with it. Therefore, the remaining money does not become unlawful for the thief or for anyone else if they acquire it through a lawful means. Repentance from theft necessitates returning the rights to their owners.