Can a brainwallet passphrase be derived if an attacker has obtained the private keys of an empty wallet.dat file?
Sorry to hear you were robbed.

An attacker cannot reverse engineer a private key to obtain the original mnemonic phrase. 

What essentially happens is just another multitude of hashes with an algorithm (SHA256). Different approaches to this are taken by different deterministic wallet generators.

As SHA256 is considered secure. So is your mnemonic phrase