It seems that an instance of DQC server is still being executed from the location you are trying to delete.
Remember that every time you try to delete a project (e.g. DQD) you first need to stop the executing instance of DQC server from that location and then proceed to delete the project.
Since most of the files have been deleted already (including the scripts you used to start/stop the DQC server) you have a set of options to stop the DQC server. A couple them are:
Windows: Open the Task Manager -> look for the Java process that is being executed -> right click on it -> end that task
DQD project: If you executed the DQC server using the generated scripts please try creating a new DQD demo project and use the stop_server.bat script in order to stop the current DQC server instance
Once the DQC server is stopped try again deleting the folder structure.