The point of sale was August 2014 which is why UEFA have allowed it. It is being paid next month because back then Valencia were under hardship and a long and protracted ownership and Spanish legal problems were being sorted. The goodwill was on City's part as Valencia wanted him but could not pay. Negredo had to leave Manchester as he, allegedly, been caught with his pants down by the wrong guy. If he had stayed, he would have gone to Valencia in installments, literally.
Yes depreciation is used by all clubs and has been before FFP, it is usually the length of the player's contract which is usually 3-4 years. That would bring City's outgoings to @£27M and income to @£20M which at £7M and is even further from £50M.