Can a variation dispute hold up handover?

Hi there,

We're about to finish a build in the first half of next year. We may possibly run into an issue with our builder, whereby there is a clause in the contract for cost increases, but there could be a dispute between myself and the builder as to the legitimacy of those cost increases and resulting variation.
In this case, can a dispute over a variation that has not been agreed hold up the handover process once the build is complete? We're happy to pay the builder the agreed contract price and agreed variations, but not any disputed ones.
Thanks for any input!

Thanks