A computer system and method that are useful for embedded operating systems, thin client computing applications and the like, protects memory blocks in a nonvolatile version of the system program used at startup (reboot), for example in flash memory. Write operations to protected memory blocks are intercepted. A potentially revised version of any attempted re-written block is maintained in RAM and can be revised further during runtime, the original protected block remaining unwritten. A restriction process flags when or whether a revised block in the RAM is to become permanent. During a write operation or at orderly system shutdown, the revised blocks that were marked are written over the protected blocks in the nonvolatile version. The process can be embodied using file and directory attributes in variably sized Ramdisk virtual drive in a Windows XP-embedded system, providing processes with read access to the original protected block as well as the revisions, enabling configuration changes and software installations without multiple reboots.