I have a pod running python image as 199 user. My code app.py is place in /tmp/ directory, Now when I run copy command to replace the running app.py then the command simply fails with file exists error.
Please try to use the --no-preserve=true flag with kubectl cp command. It will pass --no-same-owner and --no-same-permissions flags to the tar utility while extracting the copied file in the container.
GNU tar manual suggests to use --skip-old-files or --overwrite flag to tar --extract command, to avoid error message you encountered, but to my knowledge, there is no way to add this optional argument to kubectl cp.