Then goto /apps/system/config in CRXDE and double click on the factory config to check if it is the duplicate one. If yes, then delete it or move it to /tmp as mentioned by Lisa earlier.
Once done, come back and cross check that you have only single entry in configMgr which is from the application codebase.
No restart is needed ideally. The changes take place immediately since it is OSGi.
I have done that, but still, I can see the logs in system/console/slinglog. which is not the duplicated under Apache Sling Logging Logger Configuration in ConfigMgr.