`geojson.updateData()` cause existing points disappear

Nobody has claimed this yet.

**mapbox-gl-js version**: 3.6.0

**browser**: chrome 128.0.6613.137

### Steps to Trigger Behavior

1. Add a geojson data source with `dynamic: true`
2. Add a layer with the geojson data as source
3. Add 1000 points to the source with `geojson.updateData()`
4. Update one point of the source with `geojson.updateData()` burstly.

### Expected Behavior

The step 4 sometimes may cause the existing points disappear.

Reproduce Code:

```js
const map = new mapboxgl.Map({
container: 'map', // container ID
style: "mapbox://styles/mapbox/streets-v12",
zoom: 12, // starting zoom
center: [-77.432, 25.0306] // starting position
});

map.on('load', () => {
// Add a data source containing one point feature.
map.addSource('points', {
type: 'geojson',
data: {
type: "FeatureCollection",
features: [],
},
dynamic: true, // allow data to be updated
});

// Add a layer to use the image to represent the data.
map.addLayer({
id: 'points',
type: "circle",
source: 'points',
paint: {
'circle-color': ['coalesce', ["get", "color"], ['to-color', "#000"]],
'circle-radius': ["get", "size"],
},
});

map.on('render', () => {
console.log('render', Date.now(), map.querySourceFeatures("points").length);
});
const points = new Array(1000).fill(0).map((_, i) => ({
id: i,
lat: 25.0306 + Math.random() * 0.1,
lon: -77.432 + Math.random() * 0.1,
notes: `Point ${i}`,
}));

map.getSource('points').updateData({
"type": "FeatureCollection",
"features": points.map(point => ({
"id": point.id,
"type": "Feature",
"properties": {
"description": point.notes || "",
"color": point.color || "#000",
"size": point.size || 4,
},
"geometry": {
"type": "Point",
"coordinates": [point.lon, point.lat],
},
})),
});

function update() {
let s = map.getSource('points');

console.log('source', Date.now(), {
_coalesce: s._coalesce,
size: s._data.features.length,
}, map.querySourceFeatures("points").length);

s.updateData({
"type": "FeatureCollection",
"features": [
{
"id": points.length,
"type": "Feature",
"properties": {
"description": "",
"color": "#000",
"size": Math.random() * 10,
},
"geometry": {
"type": "Point",
"coordinates": [-77.432 + Math.random() * 0.1, 25.0306 + Math.random() * 0.1],
},
}
],
});
}
for (let i = 0; i < 30; i++) {
update();
}

setTimeout(() => {
update();
}, 1);
});
```

Start with the supplied browser reproduction and the GeoJSON source's updateData() entry point, focusing on the burst of updates after the initial 1,000 points. Verify the behavior in the stated Mapbox GL JS 3.6.0 and Chrome versions; done means updating one point no longer causes existing points to disappear.

Written by the indexing model from the issue text.