Does running games that is installed using cia work now?
In order for us to provide better support, we need to see the log generated by Citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File.
Yes, and it had been working? I don’t remember having issues with installed CIAs at any point of time. Or are you talking about DLC? That issue has been fixed as well. You need to redump your DLC via GodMode9.