<p>Is there any command that can be used to apply new changes, because when I apply new changes with:</p>
<pre><code>istioctl apply manifest --set XXX.XXXX=true
</code></pre>
<p>It overwrites the current value and set it to default.</p>

Shudhanshu Badkur
<p>That´s might not work because you have used <code>istioctl manifest apply</code>, which is deprecated and it´s <code>istioctl install</code> since istio 1.6 version.</p>
<p>Quoted from the <a href="https://istio.io/latest/docs/setup/install/istioctl/#install-istio-using-the-default-profile" rel="nofollow noreferrer">documentation</a></p>
<blockquote>
<p>Note that istioctl install and istioctl manifest apply are exactly the same command. In Istio 1.6, the simpler install command replaces manifest apply, which is deprecated and will be removed in 1.7.</p>
</blockquote>
<p>AFAIK there are 2 ways to update new changes in istio</p>
<h2><a href="https://istio.io/latest/docs/setup/install/istioctl/" rel="nofollow noreferrer">istioctl install</a></h2>
<blockquote>
<p>To enable the Grafana dashboard on top of the default profile, set the addonComponents.grafana.enabled configuration parameter with the following command:</p>
</blockquote>
<pre><code>$ istioctl install --set addonComponents.grafana.enabled=true
</code></pre>
<blockquote>
<p>In general, you can use the --set flag in istioctl as you would with Helm. The only difference is you must prefix the setting paths with values. because this is the path to the Helm pass-through API in the <a href="https://istio.io/latest/docs/reference/config/istio.operator.v1alpha1/" rel="nofollow noreferrer">IstioOperator API</a>.</p>
</blockquote>
<h2><a href="https://istio.io/latest/docs/setup/install/standalone-operator/" rel="nofollow noreferrer">istio operator</a></h2>
<blockquote>
<p>In addition to installing any of Istio’s built-in <a href="https://istio.io/latest/docs/setup/additional-setup/config-profiles/" rel="nofollow noreferrer">configuration profiles</a>, istioctl install provides a complete API for customizing the configuration.</p>
<p><a href="https://istio.io/latest/docs/reference/config/istio.operator.v1alpha1/" rel="nofollow noreferrer">The IstioOperator API</a>
The configuration parameters in this API can be set individually using --set options on the command line. For example, to enable the control plane security feature in a default configuration profile, use this command:</p>
</blockquote>
<pre><code>$ istioctl install --set values.global.controlPlaneSecurityEnabled=true
</code></pre>
<blockquote>
<p>Alternatively, the IstioOperator configuration can be specified in a YAML file and passed to istioctl using the -f option:</p>
</blockquote>
<pre><code>$ istioctl install -f samples/operator/pilot-k8s.yaml
</code></pre>
<blockquote>
<p>For backwards compatibility, the previous <a href="https://archive.istio.io/v1.4/docs/reference/config/installation-options/" rel="nofollow noreferrer">Helm installation options</a>, with the exception of Kubernetes resource settings, are also fully supported. To set them on the command line, prepend the option name with “values.”. For example, the following command overrides the pilot.traceSampling Helm configuration option:</p>
</blockquote>
<pre><code>$ istioctl install --set values.pilot.traceSampling=0.1
</code></pre>
<blockquote>
<p>Helm values can also be set in an IstioOperator CR (YAML file) as described in Customize Istio settings using the <a href="https://archive.istio.io/v1.4/docs/reference/config/installation-options/" rel="nofollow noreferrer">Helm API</a>, below.</p>
</blockquote>
<blockquote>
<p>If you want to set Kubernetes resource settings, use the IstioOperator API as described in Customize Kubernetes settings.</p>
</blockquote>
<p>Related documentation and examples for istio operator.</p>
<ul>
<li><a href="https://istio.io/latest/docs/setup/install/istioctl/#customizing-the-configuration" rel="nofollow noreferrer">https://istio.io/latest/docs/setup/install/istioctl/#customizing-the-configuration</a></li>
<li><a href="https://istio.io/latest/docs/setup/install/standalone-operator/#update" rel="nofollow noreferrer">https://istio.io/latest/docs/setup/install/standalone-operator/#update</a></li>
<li><a href="https://stackoverflow.com/a/61865633/11977760">https://stackoverflow.com/a/61865633/11977760</a></li>
<li><a href="https://github.com/istio/operator/blob/master/samples/pilot-advanced-override.yaml" rel="nofollow noreferrer">https://github.com/istio/operator/blob/master/samples/pilot-advanced-override.yaml</a></li>
</ul>
