Refresh data on the page which have been modified in collection

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Pretty sure you should be doing the refresh before trying to query and update the repeater from the cms with your filters.

But saying that I cannot see why you are refreshing the dataset and then querying the cms.

I would expect you to then use the refreshed dataset.
This should save you Having to re filter and query the cms again.

wixWindowFrontend.openLightbox('Ajout Suppléments')
    .then(async () => {
        let numResaValue = $w('#NumResa').value;

        // == Refresh datasets  to latest CMS data
        await $w('#SupplementsResa').refresh();
        await $w('#ResaEnCours').refresh();

        //  == wait for dataset to be ready
        await $w('#SupplementsResa').onReadyAsync();
        await $w('#ResaEnCours').onReadyAsync();

        // Now use new data
        $w("#supplementsRepeater").data = $w("#SupplementsResa").getCurrentItems();
        
        $w("#resaRepeater").data = $w("#ResaEnCours").getCurrentItems();
      
 });

Not tested…