Is it obligatory to pay the financial sums that were not deducted due to repeated lateness for work, or is sincere repentance sufficient, and who is responsible for returning this money? And how can this large sum be returned if it is obligatory to do so?

If the company's system stipulates a deduction for tardiness, and your exemption from this deduction was a personal decision by the HR manager without the administration's permission, then you must return this money to the company, unless the administration pardons you. This is the fundamental principle of repentance concerning the rights of others (Huquq al-Ibad), based on what Al-Bukhari narrated from Abu Hurairah (may Allah be pleased with him), who said: The Messenger of Allah (peace and blessings be upon him) said: "Whoever has wronged his brother concerning his honor or anything else, let him seek his forgiveness today before there will be no Dinar or Dirham." The money must be delivered to the company or its owners by any means without stating the reason if it would cause embarrassment, as Sheikh Ibn Uthaymeen mentioned.