I usually feel for people who have found out after a year that a €40 amount hasn't gone out every month and they owe that money in one go, but unless you have a very small mortgage how did you not notice immediately that it didn't go out? It would be very obvious to me if I suddenly had an extra grand in my account that's not usually there. It would mean considerable extra spending in the month for me to use this money and I don't believe I could 'not notice'. If you haven't spent it is tehre aproblem paying it back in one go.
I would imagine if you cannot afford to pay it back in one go that you could probably come to some arrangement to pay back over maybe 3 or 4 months.