I saw a theory that those 2 inexplicably red panels in Batman Inc 5 are Flashpoint happening
The beauty of Morrison's 'everything is in continuity' concept (i.e. hypertime) is that he can just say 'Sure, that happened. In that timeline over here which is just a tiny part of the stage available for MY story'. In other words, as Joker said to Batman in R.I.P.:
'but it doesn't matter see? because
every single time I try to think
outside his toy box...he builds a new box around
me'
In his story, Batman is the Hyper-Adapter, all continuity is Batman, the entire endpoint of space and time itself IS Batman.
Good luck trying to box THAT into your continuity, Johns.