Of course it'll be an issue when you come to sell the house. Not to mention being a pain having floors out of level- 60mm is a lot.
Builder may be saying 'cant jack it up, might cause more damage, destabilise walls etc etc'- well that's his problem to address and fix properly because his failure to follow instructions has directly caused it.
May be time to go legal on him- the costs could potentially wipe him out (or he could phoenix the company to duck out of the liability).
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