Expected functionality: Dropping one rune on top of another will replace/swap it in the Forge UI, similar to how it functions in the inventory.
Actual Result: Dropping one rune on top of a different type of rune adds +1 to the stack size of the second rune, converting the first rune into the second type.
Steps to repeat:
Open forge (F)
In the Modifier menu, select a rune.
Drag the rune out of the selection panel.
Open the Modifier menu and a different rune.
Drag and Drop the first rune on top of the newly selected one. This creates a stack of 2 runes (converting the first rune into the second one). From there you can remove the rune stack and re-add it to your crafting materials.