What should be done to repay a debt to a company where one worked for a short period, after exhausting direct and indirect communication methods with the employer to pay the amount?

If you have been negligent in your work, you must seek absolution from your employers or return the money you unlawfully received. It is not permissible to transfer phone credit to them, nor to give charity on their behalf with money, as long as you are able toate it to them. Strive to deliver their rights or seek their absolution to the best of your ability and seek Allah's help.