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Note that CustomUIModel page sections are not supported in ClickOnce. If you convert a custom component page section to a Custom UIModel and your application must support both ClickOnce and Web Shell, you need to leave the original custom component section intact and add an additional Custom UIModel section, setting the visibility on each section using the IsWebShell flag from the page expression model.
Figure: Leave the legacy section referencing the CustomComponent in the page spec. Add a Visible property to ensure the CustomComponent only displays in the ClickOnce Smart Client.