If I remember correctly, Masamune was no longer there in the scene where Schala warps the two party members and Magus out of the Ocean Palace.
nope, pretty sure the masamune stays there...
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EDIT::
wait, what time period is this again? is this pre- Ocean Palace incident or post? If it was post, Masamune definitely should be there....
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Zeal takes the Masamune, hits Magus, and goes away with it. Causes the whole "Masamune-less" timeline, right?
Frog still had his Masamune, and then it gets taken by Dalton later on during the Castle defense. But before that, Frog and others returned the Masamune (of the proper timeline) into the ocean depths (Old Masa&Mune talking to Masa&Mune).
But I'm still confused at the Dispatch Chambers mechanics...