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I solved this problem by move chart update into the condition
export const handleHoverChart = (myChart, x, scaleID) => {
const indexLine = myChart.options.annotation.annotations.findIndex(i => i.key === "hoverLine")
if(indexLine === -1){
myChart.options.annotation.annotations.push(convertToHoverLine(x,scaleID))
myChart.update()
}else{
myChart.options.annotation.annotations[indexLine] = convertToHoverLine(x,scaleID);
}
}
Source:stackexchange.com