// ----
function inner() {

    var doc = app.activeDocument;
    var i = doc.layers.length;
        while (i-->1) {
        doc.layers[i].remove();
    }
}

function outher() {

    app.doScript(inner,ScriptLanguage.JAVASCRIPT,[],UndoModes.SCRIPT_REQUEST,'outher');
    alert("pause");
    app.activeDocument.undo(); //<- wrong error, it actually works
}

app.doScript(outher,ScriptLanguage.JAVASCRIPT,[],UndoModes.ENTIRE_SCRIPT,'inner');

// ----

Also, this error is not ingnorable: if you put undo() in a try-clause, it doesnt work.

Alsoalso, the different undo-modes (https://developer.adobe.com/indesign/dom/api/u/UndoModes/) are NOT sufficient explained. At least write some whole sentences on how they actually differ.