what is the reason of replacing the startup-config
here is the steps :
In order to restore a configuration file to an exact copy of a file stored on a server, you need to copy the configuration file directly to the startup configuration (using the copy ftp:| rcp:| tftp:} nvram:startup-config command) and reload the router.
EDIT
same with USB :
copy usbflash0:startup-config nvram:startup-config