In this example the Oraxen Amethyst was renamed outside Oraxen, CC detects that the stack is from Oraxen and links to it.
However, we want to keep the changes, so we
shift + right-click on the result, and
shift + right-click again to open the Item Editor.
Here we select the Bukkit parser, that keeps the item as is, so it is no longer linked to Oraxen, and manual stack changes are kept.