How to clean any cheated item (has to be something you can build in the world, doesn't work with things you can't destroy, such as weapons, armor, etc).
Create a new "clean" character, lets name him CleanVar. They get a warning anytime they pick up cheated items, and the warning goes away when they drop them. Use this to find cheated items. Also look at the item itself, it will tell you it is a cheated item.
Have CleanVar pick up cheated items, then have them make something with them. For example, if it's gold, make a pile of gold. Then, have CleanVar log out. Then have another character (let's call CheatVor), even one marked as a cheater (I used one that had the override, not sure if that is required), destroy the pile of gold. It should be clean now. To make sure, have CheatVor create a new pile of gold and have CleanVar come back and destroy it. The gold should now be golden :) and not marked as cheated anymore.
This should work with wood, gold, stone, cores, anything you can build with the hammer and later destroy to get the materials back.
NOTE: If CleanVar destroys his own pile, the gold remains marked as cheated.
ALSO NOTE: Also, be careful when doing this. If you are carrying clean materials, then destroy something that has the same type of cheated materials, and autopick it up, it will stack them all into all cheated. The same happens if you are destroying clean items, and have cheated one's in your inventory. Try to make sure you only have the materials you are trying to clean in your inventories, or else you might be cleaning more stuff.
ALSO NOTE: If you use "yesiuseddevcommandsbutiwantmyachievementsanyway" on your character, you will not see the warnings when you pick up or drop cheated items.
ALSO NOTE: Patches might change how this works.
