Hi Ravi,
So, we understand, you have an existing configuration in the switch.
Now you have some commands to be added to this existing configuration without rebooting or doing a factory default.
Using a script file is a better option for this.
But as you pointed out, if you are using the existing commands in the script, it will throw the warning that the command already exists or executed.
so, try to include only the new commands to the script and execute the command
load script <.xsf file name>
If you are not able to form a script only with the new commands, we can still use your script. Even though the error comes up, the script will still execute the other commands.
Hope this helps!!