The pending flag on a folder means that the latest message from that client is an incoming one, meaning you have not yet replied to that client (within Encyro).
The pending flag may not always be useful. For instance, if normally you just receive sensitive documents via Encyro, but respond to the client via plain email, then a response may not be needed within Encyro. If "Pending" is not useful, simply click the "Hide Pending" button (flag like icon) in the top menu and the pending flag icons will disappear from all folders.
If the pending feature is useful for you but not always, such as some clients were sent a response outside of Encyro, then on those clients' folders, you can access the latest message in the folder, and from the drop down menu (three dots) near the "Forward" button, select the option to change the pending status.