I don't see how you and your family can have it both ways:
If a second charge is put upon a property, it is basically a method of surety such that if 'the loan' isn't paid back, the 'lender' has a means of getting the money back when the property is sold.
One either gives money to the family or one gives money with strings attached. In this situation there are strings attached - HMRC will treat this as a 'gift with reservations'.
So, I believe that the financial organisations involved in your property are correct in treating this as if your family lent you £10k - which is actually what happened, albeit over a period of time - not a gift.
You don't say whether if he cancelled it your father also wants his £10k back at the same time. By cancelling it he would be writing off the security that he has against the loan, but that doesn't mean he has to have the money back - it just becomes either a unsecured loan, or a gift.
Irrespective of all of that, if he is claiming credits for being on low income, he would have had to declare this 'loan' and its circumstances - then let the authorities decide what impact it has on his claim. You are saying that he did that.