Regarding the matter of the multiple appearances of Sephiroth's Masamune, certain events in Advent Children seem to put an end to that apparent issue. In AC, major Advent Children Spoilerwhen Sephiroth is able to again realize himself on Gaia, he also "rematerializes" the Masamune out of thin air. Given that he demonstrates such an ability, it seems likely that he could have left the Masamune anywhere, only to again manifest such a blade as needed.