Select Multiple Objects then Paste much like the Place command with multiple files Illustrator

here's a basic test case script that will replace placeholder items in Layer 1, with source items in Layer 0 (top layer)

set up you test file like this

the script will match each Layer 1 placeholder item's size and position to each Layer 0 source item, then it will remove the placeholder item

result

// replace placeholder items
// place source items in layer 0
// place placeholder items in layer 1

function main() {
    var idoc = app.activeDocument;
    var sourceLayer = idoc.layers[0];
    
    // if first layer is empty, then skip
    if (sourceLayer.pageItems.length > 0) {
        var sourceItems = sourceLayer.pageItems;
        var sourcecount = sourceItems.length;

        var placeholderLayer = idoc.layers[1];

        var placeholderItems = placeholderLayer.pageItems;

        for (var a=sourceItems.length-1; a>=0; a--){
            sourceItems[a].width = placeholderItems[a].width;
            sourceItems[a].height = placeholderItems[a].height;
            
            sourceItems[a].position = placeholderItems[a].position;
            sourceItems[a].move(placeholderLayer, ElementPlacement.PLACEATEND);
        }

        // REMOVE PREVIOUS PLACEHOLDER ITEMS
        for (var b=0; b<sourcecount; b++) {
            placeholderLayer.pageItems[0].remove();
        }
    }
}

main();