Okay, this is odd, as I expected.
First, this track should've never been a thing. It was from a build before I released the game... The final boss theme was changed right before release, and this is probably the first complain I have for this specific error to appear. During that I've personally cleared the game twice without this glitch to appear, and no one, even those who I knew have completed the game ever met this glitch.
Second, you CAN save after leaving the SDM. Keine gave you an even more powerful scroll than what you've been using so far. Look for the Great Hakutaku Scroll in the inventory. You cannot start the final sortie unless you talk to Keine and get the scroll from her, so I believe it should be in the inventory.
Back to the track though, it's weird. It's like you somehow got the version that I have sitting on the Recycle Bin when I uploaded the game... a few months ago. The one that was NEVER uploaded... What is going on here?
I'm not joking, this is legit weird stuff...
Anyways, I would suggest downloading a fresh copy and transfer you save files there, but this might be worth a try first.
If it doesn't though, please screenshot the scene before the error pops up. That can narrow the problematic script a bit.
I won't update the official Bug Fixes just yet, because I really hope this is an isolated case. Good luck.