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We are building multi-tenant INTRANET application so we can't ask the client include the app package in their appcatalog often. So we tried this, 1. Maintained the track of the bundle file name and on new builds renamed the bundled file. 2. To avoid the files cached in the CDN we have used deploy-azure-cdn npm command and set the maximum age for caching file to 1 minute so everytime they refresh the page it will get the latest version from Storage container. Since our bundle files are small in size there is no major latency.
Resolved the issue by reordering the custom scripts added in the master page. Previously the custom scripts were added in Body tag and I moved it to head tag the issue resolved now.