What is the ruling on using mosque funds to pay off personal debts, then returning them in full after a period of time, and is that considered a sin?

Your father is not permitted to borrow from the endowment (waqf) money for his personal use, and he must repent for what has passed, because the supervisor (nazir) of an endowment is not allowed to take anything from its funds as a guarantee. Lending from endowment money is like lending from an orphan's money. Similarly, he is not permitted to buy or rent from the endowment for himself, his father, or his child, due to the possibility of favoritism. However, the supervisor of an endowment is allowed to take a customary fair wage from its funds.

It is important to note that attributing will (mashiyya) to circumstances is incorrect; it should be attributed to Allah alone.