Rowena's loft is located at 'The Aradia Apartments' building. It's situated at least a few hours from the Men of Letters Bunker. It appears to have been first inhabited by Rowena following her second resurrection. At some point before her death, Rowena placed a very powerful and potent hex on the apartment, causing anyone who steps inside to die. The spell seems to have had exceptions built in for Sam and Dean Winchester.
While the main part of her apartment was filled with various self-help books and a few magic paraphernalia, Rowena kept all her treasured spells, ingredients, and journals locked away in a hidden room behind a bookshelf.