As indicated in another answer, the error you get is exactly the same as you when you try to connect the debugger a second time when it is already connected.
At the same time, if this does not explain your case, look at this line when you first start the application through Run As --> Application.launch :
Listening to the dt_socket transport at: 8000
It tells you on which port it is listening for possible JPDA connections, and if this line is missing, something is wrong. You can change the configuration of Application.launch manually (look at the address parameter of the -Xrunjdwp parameter passed to the Java virtual machine) and change the port if necessary. If you make changes, you also need to update the Connect JPDA to Application.launch launch configuration.
In any case, this is my suggestion - make sure that the application really listens for possible debugger connections and try changing the port that is used for this purpose.
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