Deployment package + copy and replace file

I need to create a deployment package for Cisco that once installed it copies and replaces a file with the same name while making the package available for the users to download and install it themsleves.

The file is a config file that needs replacing so it has the updated vpn settings etc. I know how to copy a file using a deplyment package but the file it is replacing wont replace it using a task as the file is in use so it stops the job from copying and replacing the file. The developers have advised that if we install the exe and then copy and replace the file.

Whats the best way to achive this while still having the option for the users to download and install it themselves.