This topic is a little dated, so to update it a bit:
The original discussion dealt with an old method of persiting registry changes called the RAM based registry. In the RAM based registry, any call to RegFlushKey() caused the entire registry to be saved to flash ROM.
Eurotech currently supports the HIVE based registry. In the HIVE based registry, the registry is saved in multiple files in a file system, like FlashFx Disk. I recommend that to be safe, RegFlushKey() should be called twice; once with HKEY_LOCAL_MACHINE and again with HKEY_CURRENT_USER. This is what Microsoft does when the system suspends and what we do in \Windows\RegFlushKeys.exe.