That is a good question. There's enough space left that you could actually run one app which flashes and loads another app. Not an overnight thing, but we have allocated a little bit of space for future potential on-chip storage...so that might help along the same lines.
The other thing we may be able to do with this board: local deployment/debugging over Ethernet. There were some issues with the lwIP implementation that prevented this, but it may be possible with NETMF 4.2/4.3.
What about using the SD card for flashing new deployments? If our user code saves the firmware to the SD card and sends a reset signal, could the firmware auto-deploy user code or firmware from that image?