I picked up the horde warbanner from xroads, then went to silverpine and got the endless rage rune there …
If i use the rune from silverpine will i lose the ability to use the horde banner at the barrens
(Will the warbanner and xroads vanish?)
Most likely yes. Shamans can use the totem that spans at place where lightning hits the ground to gain relic that upon completing it’s objective transforms into a rune. After it is do you can not use that totem if you encounter one in the open world again.