By the way, I just did this also -- it took more than 30 minutes, because the upgrade had already cleared (my parents did not want the upgrade due to cost and lack of reimbursement from their company). Also, the agent at first suggested that there would be a miles redeposit fee. But then went away for another 5 minutes and it was waived. So it just takes a long time.
And the agent (or a supervisor) would have had to bend the rules for this. The fee is to re-deposit mileage, whether for a full award ticket or an upgrade, is supposed to cost whatever the fee is based on status. If you are a plat or higher, then it doesn't matter, but for gold or lower, getting an agent to waive it is absolutely a favor, and isn't necessarily going to happen. Buyer should beware, I gues.