What should the questioner do with the remaining amount she took from her colleague 13 years ago, and should she give it as charity on her behalf, or return it directly to her, or add to it due to the passage of this period?

Overtime work and its wages are your right, and it is not forbidden for you to take the payment if you take your colleague's right. You are not obligated to pay her the wages. This is closer to an "Ijara (rental/leasing) bargain," and the contract is valid in this case. You must repent, seek forgiveness, and supplicate if you are unable to seek your colleague's pardon.