Another post describes how individual funding agreements could be amended by agreement between the Secretary of State and the Academy Trust.
But, of course funding agreements could be overriden by acts of parliament.
We now have the first example of this with the new regime for exclusion reviews (i.e. the loss of the right to appeal to an independent appeal panel to challenge a permanent exclusion) being extended to academies though regulations which override existing academy/free school funding agreements. See here for more information.
That overrriding means that many existing academy/funding agreements are now out of line with the wider law.
That makes it harder for anyone trying to work out what the rules are in an academy/free school.
Not only do you have to look at what is in the funding agreement and what additional things are imposed by the law (such as equality or human rights obligations) you also have to worry about what in the funding agreement may have been overriden by the wider law.
A can of worms.