For a case like this, the investigator doesn't recommend one way or the other. That decision is reserved for the law side to take care of. The FBI and prosecutor work together, ostensibly to insure that the prosecutor doesn't bring a case on evidence the investigator can't produce. Of course the investigator is sometimes miffed at a decision by the prosecutor (cops in FLA were unhappy Angela Corey charged Zimmerman, for example - and the FBI was unhappy that DOJ gave Petraeus a plea bargain), but they have nothing but persuasion to work with. The prosecutor has 100% of the legal power, and has discretion.
Separately, just a news tidbit, Catherine Herridge on FoxNews just said she's never seen such aggressive damage control in the 15 years she's been a newsie.
For a case like this, the investigator doesn't recommend one way or the other. The article says otherwise =>
Attorney General Loretta Lynch has decided that she will accept the recommendation of the FBI regarding its investigation of Hillary Clinton’s e-mails.