Why would it delete the code after uploading it ?
Resetting the board does not delete the code it just starts the processor from a known point so that it can go through its start up routines to set up its hardware before running the code
Whilst I agree that the
Hard resetting via RTS pin...
message is a little open ended, by the time that you have seen it the reset is complete and your code is running. So, you can safely unplug or power down the board at that time