Hey Ravi,
If I am understanding correctly, you have a configuration file but you would like to use a different configuration file. Is that correct?
If so, there is no need to remove the old .cfg files. Once you upload the new configuration file to the switch you can tell the switch to use the specified configuration file by running the command "use configuration ". You will then be prompted with the following:
"The selected configuration will take effect after the next switch reboot."
Once you issue the reboot command the switch will come up with the new configuration.
Please let me know if I'm misunderstanding your issue!