EXACTLY. Just like how Calamity Trigger almost had NO REAL BEARING on what happens in Continuum Shift. As soon as I saw that Hakumen was still around in CS, I was like "That is rubbish, I am POSITIVE that Ragna killed him in the True Ending." but I let that slide because Hakumen is one of my favorite characters, but the point being ANYTHING CAN HAPPEN.
EDIT: Sorry, this is just me ranting about how random BB's story is, how inconsistent it is. I'll stop right now. I know that there's time paradoxes and shifts and crap like that but good god, they're trying way too hard.