Just because Final Crisis
didn't happen, that doesn't mean that Darkseid didn't send Batman back through time, it just means it happened in another way.
Yeah, that's reaching.
The only way any of the Batman stories make sense in the new 52 is if Batman Inc is considered not to be a part of it.
Once again, DC f***s up a reboot, despite Jim Lee's saying that they were not going to f*** it up.