How do I clear memory after a save()

Yes, it's a bit odd, but:

If Espruino is loading from flash (even if it is loading empty code written by save()) it doesn't display the logo... So pretty much the only way you get the logo displayed is right after you update the firmware :)

The reason is that if you've saved anything and you connect to a PC, you want to print as little text as possible in case the PC isn't listening to what's being printed - because if the PC isn't reading data, output buffers get full, and the code halts waiting for it to empty again.