Answer

To delete a project from FlexiCapture 11 server please do the following:

1. Stop the Processing server.

2. Open Administrator & Monitoring Console with administrator rights and close all current sessions in Monitoring > Sessions.
3. Make sure that there are no important data in the processing, then select all active sessions and click the Delete sessions button. 

4. Go to the Application Server menu item > Service >  Application Server  > click the Refresh button.  Then select a project you want to remove and click the Delete project button.