I was using the mobile site and I paid the full contract amount as a bonus and my account is now showing a balance due. How do I delete the balance due since the contract was paid via bonus?
The only way is to pay the amount due on the contract, and then ask the freelancer to refund the bonus you paid.
Upwork cannot do this automatically for you, because it's possible for the bonus to be part of an agreement you had with the contractor. If they did additional work for you that was not part of the initial contract, you could have decided to pay for it as a bonus.