Will a person be sinful if their father's grave in the Levant is not in accordance with the Prophetic Sunnah, knowing that there is a Prophetic hadith commanding the leveling of graves, and that the cemetery system in the Levant differs from the Gulf in terms of buying, selling, and official ownership?

The Prophet's guidance (peace be upon him) was to level graves and not to build upon them. Therefore, it is obligatory to level the grave so that it does not exceed the prescribed height, and it is obligatory to remove any structure built upon it, if found. If you are able to level the graves of your parents or others without harm, then you must do so, and you will be rewarded for it. However, if you fear harm, then do not do it, and there will be no sin upon you in that case due to your inability to remove the evil.