Is it obligatory for someone who repaired their tooth with ill-gotten money and repented to remove the material they affixed and re-affix it with lawful money? And what is the general rule in such a case?

It is not obligatory to remove material purchased with ill-gotten money, because the ill-gotten aspect is tied to the purchaser's liability, not to the material itself. He must repent and give out the equivalent amount of the ill-gotten money. If he knows its owner, he should return it to him; otherwise, he should give it as charity.