Are you trying to add a control flow between two Application Components?. (by modifying the ArchiMate technology) or are you trying to extend the Application Component as something else (say Application) and add a Control Flow between
Below is an excerpt from my custom MDG where Application(extended from Component) is connected with a ControlFlow
//Source Element Type,Source ST filter,Target Element Type,Target ST Filter,Diagram Filter,New Element Type,New Element ST,New Link Type,New Link ST,New Link Direction,New Link Caption,New Link & Element Caption,Create Link,Create Element,Disallow Self connector,Exclusive to ST Filter + No inherit from metatype,Menu Group,Complexity Level,Target Must Be Parent,Embed element,Preceeds Separator LEAF,Preceeds Separator GROUP,DUMMZ COLUMN
Component,Application,Component,Application,,,,Controlflow,,to,MY_Control Flow,,TRUE,,FALSE,TRUE,,0,,,,,
PS - if you are intending to modify the default ArchiMate MDG, you have to insert this one line in your QL text from ArchiMate technology