Just read a handful of articles -- I think the approximate timeline / subtext is as follows;
The FBI started investigating a kickback scheme from a State Senator (Jon Woods) who was steering contracts to a small school in exchange for cash and payments to a nonprofit he ran from school administrators. They quickly 'flipped' one of the admins at the school (Micah Neal) who agreed to provide evidence to the FBI in exchange for a guilty plea and reduction in his own sentence.
Neal offered to start recording conversations with Woods, but the FBI told him they didn't want him to / need him to (presumably because they had enough written evidence and financial detail to make the case). Neal recorded 119 conversations anyway and gave them to the FBI.
When the DOJ indicted Woods, his attorneys would be given all investigative material and the FBI agent in question sent him 39 audio files. Woods' attorney realized there were missing files, so he had the court force the FBI to turn over the rest of them, and that's when the FBI agent went out and erased the laptop.
Reading between the lines - the FBI agent probably sent the most 'damning' recordings, left out anything that would impugn their witness, and then panicked when he realized he was caught. The DOJ didn't use the recordings at trial and hadn't asked for them, so I suspect there was no greater motive in the deletion than trying to preserve the conviction/investigative effort.
Corrupt Senator wasting taxpayer money goes to jail, bad FBI agent goes to jail, all seems fine in the end.