More information needed.
Are you able to be more specific about the details of what you are trying to do?
What software, script, commands, etc. are you using to copy the files?
For the most part there is likely some option that can be set to overwrite without further end user input.
Maybe a default value that makes the decision one way or another. I.e., Overwrite /Do not Overwrite. Warn, confirm, OK, Yes.....
Whatever deters the need for additional user input be it keyboard combinations or simply the click of some option button/choice. Yes/No, Overwrite: Approve/Disapprove. Basically asking you to decide and how the file copy will proceed.
And all you may need to do is set that default value to what ever is required to simply do the overwrite without any further end user input.
In Powershell, for example, there is -Force parameter that does just that.