The short answer is that funding agrements could be amended (e.g. to keep up with the requirements of the latest model agreement) but that would require the agreement of the academy and, in practice, very few (if any) seem to have been amended in that way.
As seen from the copies of Funding Agreements on the Department’s web site, most funding agreement remain in the terms in which they were originally agreed, ‘warts and all’.
I have been told that the Department has proposed amendments (perhaps on more than one occasion) to try and bring them into line with the more modern ‘model’ agreements. But academies have apparently refused (as a party to any agreement is generally entitled to do) to agree changes.
One notable exception is where some structural change created a wider need to amend a particular Funding Agreement.
That happened when the agreement for Haberdashers Aske’s Hatcham Academy had to be amended in 2008 when the Academy expanded to absorb Monson Primary School. At that point, the Department took the opportunity to improve the provisions in the contract relating to various things including appeals against permanent exclusion. However, it also removed the limited ability previously enjoyed by the Haberdashers Aske’s Hatcham Academy (and enjoyed by all maintained schools: School Standards and Framework Act 1998 sections 86-87) to refuse to admit a pupil who had been permanently excluded from two other schools.