We are currently using RoboHelp10, and when launched locally in Internet Explorer, users see the popup requesting them to Allow Blocked Content. If they don't allow the blocked content, the index and search functions in the sidebar don't work properly. We have tried to get rid of this popup by adding a Mark of the Web comment, but when we did this we were unable to open pdf files in the WebHelp. Is there a way to avoid having this popup, but still have the sidebar, and all other parts of the Webhelp, function properly?
In IE Options > Advanced there is a setting Allow active content to run in local files. If that is ticked you will not get the warning. However that applies to all active content, not just your help. Are the users in your company or are they external users? If the latter, you cannot control their settings.
Another option would be to use Multiscreen HTML5 but that would change all the calls to your help. That output can run locally or from a web server.
See www.grainge.org for RoboHelp and Authoring tips
Wow, where are your users running WebHelp from? I'm guessing it's a LAN server? Are you able to move it to an intranet web server? If you did that, they wouldn't see the warning.