Hi Rohit Pathak,
If you start CQ using the script crx-quickstart/bin/start, then the file crx-quickstart/sling.properties is used when CQ start up. However, if you start using the jar file (e.g. java -jar cq5-author-4502.jar), the file crx-quickstart/conf/sling.properties is used instead. If the sling.properties does not exist for any reason, it will automatically create a default one.
Thus, depending on how you start CQ, it will determine which sling.properties is used. You can remove the one that you do not need.
Thanks,
Sham