This sounds like The Cookie Monster by Vernor Vinge.
The story follows Dixie Mae Leigh, who is working in customer support for a large hi-tech company, LotsaTech. She gets an offensive email from somewhere else in the company and decides to track the sender down to give them a piece of her mind. She enlists the help of some co-workers to help, and they gradually realize that the email is a cleverly crafted clue to what's going on at LotsaTech. In the end, they discover that...
They are all simulations of real people, being run at high speed to provide brainpower for the owner of LotsaTech, Gerry Reich. In the real world, he's using inventions and discoveries made by the simulations to make himself rich. The simulated people simply get rebooted every day so that there's no need to provide a simulation of their home lives, social lives, etc. The email was sent by an earlier iteration of Dixie Mae and was worded so as to make her later iteration angry, starting the whole chain of events.
The story was originally published in the October 2003 edition of Analog and has been republished several times since then. It won the Best Novella Hugo in 2004.