What is the ruling on money earned from a government job where one does not adhere to its work hours, and must this money be returned if the non-adherence was overlooked?

There is no harm in your past appointment before fulfilling the requirements, as long as you performed your work as required. As for the days you were absent or late for work, you do not deserve the corresponding salary for them, and the forgiveness of the official is not sufficient. The way to absolve oneself is to take out the equivalent of those times from your salary and return it to the financial authority. If you know that they will not put it in its proper place, then spend it directly on public welfare, such as for the poor and needy. If you pay out this amount, then there is no blame upon you regarding the profit resulting from your work nor regarding the possessions you bought with it.