Just an update, the contractors have agreed to replace the tiles in high traffic areas which will probably be about 50% of the floor area.
A third party consultant did a spec for refixing the tiles and recommended an uncoupling membrane like ditra. Given that not all the tiles will be taken up to keep the floor flush I'm limited in the height of the the current adhesive bed which is about 7-8mm. This seems insufficient to have anything besides a solid bed?
In addition, there are a few sections of the screed now that have some grooves from when they were a little aggressive in taking up the tiles. Is it ok to simply fill those with adhesive or should they be levelled off with more screed?