Is it necessary to follow up on the book's price deduction after its shortage has been proven, and to follow up on the deduction of leave days after the father's death, or is what has been done sufficient?

Since you have advised the official and the book has been recorded in the certificate of clearance, you have fulfilled your duty. You are not required to follow up on the institution's procedures or the amount deducted from the leave. However, if you become aware of an error in calculating the leave period or in not including the price of the book, you must alert them to the error.