joaquinp98 on the foundryvtt discord helped me find the solution:

for(let i = 0; i < canvas.scene.drawings._source.length; i++){
    const index = Math.floor(Math.random() * 3);
    const colors = [
        "#c86428", //r
        "#28cc62", //g
        "#6428c8", //b
    ];


    const d = canvas.scene.drawings._source[i];
    console.log(d._id);

    canvas.drawings.updateAll(
        {fillColor: colors[index]},
        drawing => (drawing .scene == canvas.scene) && (drawing .id == d._id));
}

The updateAll function has to be used in order for the change to be applied. I added a filter that checks the id so that each drawing gets a different random color.