I'm not sure I understand what you mean here.
I thought BleachBit completely erases the data, so that there would be nothing for a hacker or the FBI to find, once the erasure had been done. Or are you saying that there still is a way to detect faint traces of previous states of each "bit" of data before the erasure?
Encryption, on the other hand, does not erase the data, but just encodes it in a way that is difficult to decipher.
I think the most likely scenario is that Hillary had her server completely erased (except for the part that the computer specialist forgot... the "oh, sh*t moment" referred to in the Times article), but before it was erased, transferred the data to memory sticks that only she and Bill know about and have access to.
Of course, any number of hackers could have gotten the emails before they were erased. That's her big worry between now and Election Day.