The "Swap runes" service is located in the blacksmith's customization section and allows you to swap runes of different items you own (whether equipped or in your backpack) at the blacksmith.

To swap runes click on an item or drag it onto the corresponding area at the blacksmith or use the right-click context menu on the item whose rune you would like to swap. A window will open where you can select the target item and rune. Now select an item you would like to use to swap runes. Items which could be used will be highlighted in your backpack.

Swapping runes costs 20 mushrooms.