BOA gear is a diffrent story. I was able to upgrade the 463 staff and trinket that were obtained through arechology. They are now 471, and are a great help to leveling my cross faction toon
Does anyone know if this will work with the BOA scribe staff?
I can confirm that upgrading an item with Justice/Valor does not remove the gems, enchants, reforging, or transmogging: it just seems to update the stats. As degias said, this works on the arch staff as well (my monk loves my 'lock for that).
I don't know about the Inscription staff, but I would assume it works the same way.