What is the ruling on sending final accounts to the employer stating that the bank account is not deficient, knowing that an amount has been withdrawn from the branch to pay bills for other branches, and the deputy manager promised to return the amount later?

It is not permissible for you to record the accounts as complete when they are not, because that is deception. Fear of the wrath of the rightful owner does not justify this action. You must explain the matter as it is; otherwise, the right of the rightful owner will be lost due to your complicity with the deputy manager. You are entrusted with the accounts, and part of the trust is to preserve them and act upon them according to what the entruster has commanded, and he would not approve of this action. Therefore, do not yield to the deputy manager and explain your excuse to him.