We finally fixed the issue by moving the app configurations to the default directory and letting customers use local directory for creating dashboards. Additionally, we have added excludeFromUpdate option for the local directory.
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I did use that but it didn't work. I've raised another question regarding that. Please check https://answers.splunk.com/answers/521791/why-is-the-link-not-getting-displayed-in-the-dashb.html
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