NASA's future deep-space missions will require onboard software upgrade. A challenge that arises from this is that of guarding the system against performance loss caused by residual design faults in the new version of a spacecraft/science function. Accordingly, we have developed a methodology called guarded software upgrading (GSU). The GSU framework is based on the Baseline X2000 First Delivery Architecture, which comprises three high-performance computing nodes with local DRAMs and multiple subsystem microcontroller nodes that interface with a variety of devices. All nodes are connected by a high-speed fault tolerant bus network that complies with the commercial interface standard IEEE 1394. Since application-specific techniques are an effective strategy for reducing fault tolerance cost, we exploit the characteristics of our target system and application. To ensure low development cost, we take advantage of inherent system resource redundancies as the means of fault tolerance.