I just know that if Ragna is somehow related to this "Bloodedge" person Jubei refers to or if he is in fact Bloodege from an timeline (by travelling backwards), we've got a bigger loop on our hands than first thought.
Likewise, anything to do with Haku-men seems to be an error in the time stream from that point (Continuum Shift) on. Haku-men mentions Ragna "beat him before" but that was past tense, referring to the events of CT. It has never once been suggested that Haku-men was killed. If anything he was blown away by Ragna's Blood Kain only to survive embedded in some debris and recovered by Kokonoe only to be retrieved by Rachel.
In my experience with Guilty Gear storylines...it's not so much the plot that makes sense in its entirety, but the characters and how they interact with it. Alternate endings can still be partially true, even if they are alternate endings.