Most likely, yes, but that is a really broad answer. It is possible to erase a hard drive to Department of Defense level standards, with programs that you can easily buy online. I doubt she, or her staff, did that.
Recovering information is best done the first moment you realize it's been lost. So if she deleted something in 2011, and then continued to use the server for several years, it is unlikely that someone would be able to recover that deleted item from 2011.
Although I think this is a terrible breach in protocol, and was not a smart decision, it is my understanding that the general public doesn't understand clearance very well.
It's been explained to me that many times an item is marked classified it is not because it has some juicy secret, but the method that information was collected needs to be protected.
For example, if someone had put a listening device into a phone of a high level target, and that target made a call and placed an order for a pizza, someone might document that call and mark it classified. Not because the pizza order is particularly important, but because the listening device's existence needs to be protected. Is that correct?