Batman is capable of doing many things. He has a contingency plan for everything. He is a master at pretty much everything he does. Batman will also go to extreme means to protect those that are part of his inner circle.
For members of the Bat Family, the secret identity is a crucial element in their fight against evil. There is too much at stake to allow this secret to get out. Batman has the means to create new identities with minimal effort (he provided the paperwork for Supergirl and Christopher Kent without a problem).
With Batman, Incorporated, Batman has agents all around the world. When sending agents undercover, Batman will ensure they are fully protected. Before 'The New 52' caused some tweaks in the DC Universe, Batman sent Stephanie Brown, under the guise of Batgirl at the time), to go undercover at St. Hadrian's Finishing School for Girls. Was Batman careless with her secret identity when sending her off? (There will be some minor spoilers from BATMAN, INCORPORATED: LEVIATHAN STRIKES).== TEASER ==
Recently in the pages of BATWOMAN, Flamebird was badly beaten. Left for dead, she managed to survive but was taken to the hospital and there was an attempt at discovering who she was under the shredded remains of her costume.
Because of her past association with Batman, there weren't any records of her existence. Fingerprints, DNA and the works have been wiped clean from all records. This is simply something Batman does in order to protect the heroes and to protect his own secret identity.
Yet when sending Stephanie Brown undercover, she didn't use an alias. She went using her own identity. This made sense as she was already in college in Gotham City. But knowing, or at least suspecting, there was something going on at the school (thus the reason for sending Stephanie in), it doesn't make sense that Batman would risk Stephanie's personal secret identity.
At the school, the other girls (in the secret organization they were investigating) immediately suspected there was something more to Stephanie. Somehow the word had gotten out that she was suspected of being the daughter of Batman. How and why this assumption came about wasn't explained. Stephanie had to prove her fighting skills in order to be considered to be brought in to the group, which was part of her mission.
When Stephanie was being prepped, her records were looked at. They knew her name was Stephanie Brown. They were able to pull up her history and found out her father was Arthur Brown, the Cluemaster. When Stephanie's infiltration plan didn't quite go according to plan, she had to act openly and upon escaping, put on her Batgirl outfit. In other words, everyone would soon know that Stephanie Brown was Batgirl.
Stephanie is no longer Batgirl. It was thought she would simply go back to her Spoiler identity. Even though the school's evil plan was uncovered and Batman arrived to clean things up, Stephanie's identity had already been compromised and who knows who else was privy to the information.
It doesn't seem likely for Batman to have her use her own identity. Being the daughter of a former supervillain gave her a needed edge to try to infiltrate the organization. It just doesn't seem necessary as Batman could have easily created a new identity to her and even tied her to some other deceased former villain if he really wanted.
Where is Stephanie now? That's one of the big questions since 'The New 52' began. She's not using the Batgirl identity. It might be hard for her to try to have a normal life when her life and her mother's has been needlessly put at risk. It's possible Batman erased any electronic evidence at the school but he can't erase the minds of those that were there.