I'm certainly no expert on this subject, but I think I can give you a basic answer to your question anyway.
When your computer first starts up, it looks for a folder that contains the Macintosh operating system. The folder ID number is stored in the boot blocks of the hard drive. So, it first checks the boot blocks to see what folder, if any, has been specified as containing the operating system.
If a folder has been specified, it looks in that folder for the System and Finder files. If found, it will use the information in these files to continue the startup process. If one of these files cannot be found (missing or corrupt), it will display a flashing question mark on a disk.
Now, if the System or Finder files have been replaced (or sometimes even for unknown reasons) you will probably need to re-bless the System Folder. "Blessing" the System Folder means identifying the folder containing the Mac operating system and writing that information to the boot blocks. A blessed System Folder will always have a custom icon: a small computer (older systems) or the Mac smiling face.
More information about the boot blocks can be found in Apple's TIL #3082. If interested, here's the URL:
Hope this helps a little anyway,