One example - and this generally only comes to light when there is a dispute - http://sportwitness.co.uk/manchester-city-demanding-payment-transfer-refuse-renegotiate-terms/
Sometimes clubs will negotiate a reduction in the fee to pay off the remaining stage payments sooner - sometimes they will agree to pay extra in order to reduce the size of the payments due - sometimes a club will accept a renegotiation out of the knowledge that the other club could go bankrupt and they will get little or nothing. It is normal business practice - and, after all, football is a business.
So a story about Man City not willing to renegotiate is your example to support your assertion that many fees are renegotiated!!!!
I'm pretty certain that that is a rare occurrence in the England.