I was researching a way to do major router changes remotely.  I found that if I tftp’ed a new configuration directly to NVRAM and replaced the startup-config file, then reloaded the router, all changes would go into effect.  While testing this process locally, I found out that when the router was reloaded with the new configuration file, the SSH encryption keys got erased and had to be regenerated.  So if this process is used, make sure telnet is enabled on the VTY lines so that you can get back into the router!