Javascript issue

You can't declare "controls" variable multiple times. You have to use different variable names for each object. There are three options to do it:

Option 1
It updates your initial code

let controls01 = document.querySelector("[data-model-id='60O8MBAYLcA']");
controls01.style.zIndex = "9999";

let controls02 = document.querySelector("[data-model-id='689jgbOitBP']");
controls02.style.zIndex = "9999";

let controls03 = document.querySelector("[data-model-id='6R7jmOoLVUg']");
controls03.style.zIndex = "9999";

Option 2
A more efficient way to avoid redundant, repetitive lines of code from Option 1

let controls = ["6QRrSIXWFTI", "5o24oXaoCNj", "5jkOK4Yq1d3"];
controls.forEach(control => {
    let controlId = document.querySelector(`[data-model-id='${control}']`);
    controlId.style.zIndex = "9999";
});

Option 3
If possible, group all objects on the master slide and use the data-model-id of the group.

let controlsGroup = document.querySelector('[data-model-id="6lNdgNGW4o0"]'); 
controlsGroup.style.zIndex = '9999';