But we clearly see the Masamune get destroyed. And if they did fuse, you have that negative energy to worry about.
I didn't see it get destroyed, I just remember the Sea Swallow flying up to the Masamune, then the Mastermune appeared.
The Masamune does float in the air and suddenly explodes, and after that you don't see the sword anymore but Serge's swallow. You might have forgotten maybe (I didn't even notice until my fourth playthrough or something). What really makes people not think it got destroyed is what the characters say after the "explosion":
Radius:
Hmph!
It appears the Masamune
found a new master.
Karsh:
What!?
Lynx!!!?
Radius:
Do not panic.
Look around you.
Riddel:
Birds...!
The birds that fled
are coming back!
Radius:
I no longer sense the slightest
bit of malice from the Masamune.
There is no more fear of
succumbing to its enmity.
They speak totally as if the sword was still there, even though we do see it go boom. So... maybe the explosion was the sword's evil form getting destroyed, and there was the normal sword after that that the lazy developers just didn't showed (they were even lazy enough not to show Masa, Mune and Doreen
).
After all I said in my previous posts, I start to think the sword didn't got destroyed but physically fused with the Sea Swallow (would be such a shame if not!).