A full run contains three missions followed by a World Boss. Returning to Sanctus Clypeus between those missions does not end the run, so the Loadout Station stays unavailable until the run is completed or you die.
Run structure
Official guidance defines a full run as three missions followed by a World Boss. Returning to Sanctus Clypeus between those missions does not end the run, so the Loadout Station remains unavailable until the full run is completed or the Nephilim dies.
Verification note
Official sources define intended behavior. Community timing and bug reports are labelled separately and can change after patches.