Yes. Here's part of Obama's response, quoted in the Associated Press story above:
"Did she use a personal email account for government business? Absolutely. That's something that, again, I want to leave to the Justice Department, to go through," Obama said. "It was a mistake to do it. As soon as possible, I want her to say whether she used it for official business or personal communications. You know, all sorts of reasons exist for not doing emails. I don't think there's any doubt that she did use them for business-related purposes; that she did not have a government email address."
So, Obama actually knew Hillary's secret server. He knew it was used for personal communication. He knew it was being monitored so he could see if it was being used against her, and so he wanted to know, and Hillary wanted to tell.