What should I do about the money owed to the Ministry of Health, which I have been unable to pay due to the loss of the contract file?

What is obligatory upon you is to refer to the officials in the Ministry. If they permit not paying the amount, then there is no blame, and the accountant's word is not sufficient. However, if they demand it from you, then you are obliged to pay it, for the Prophet, peace and blessings be upon him, said: "Muslims are bound by their conditions." If you cannot reach the officials and find no way to pay the amount, then spend it on the poor and the needy.