Just an idea: As far as I understand, the Daisy bootloader can load a .bin file from Sd card. So if you rename and restart, you could read different software without a raspi.
Hi again,
what you might want to study is DFU-UTIL (sourceforge.net)
This tool is used by Plugdata to download to Daisy. It can both download to internal or external flash.
cheers. For internal flash:
dfu-util -a 0 -s 0x08000000:leave -D Progname.bin -d ,0483:df11