In office 365, you can change the SharePoint Site Alternate CSS Property using CSOM Code. In this way, you can customize the host web’s alternate URL using Provider hosted model. Below are the sample code to change the SharePoint Site alternate CSS property using CSOM code.
// Get the Web Object from the Client Context.
Web web = clientContext.Web;
//Update the Alternate CSS property
web.AlternateCssUrl = web.ServerRelativeUrl + “/SiteAssets/mycustom.css“;
//Execute the query.
Please make sure that your customcss must have been uploaded to Asset Library before executing the above Client Side object Model code.
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