The kernel is stored in flash. The player software (and other OS stuff) is stored on the hard drive. When you install new player software, it installs both, but only installs the player software on the primary drive. If, for some reason, the drives were swapped, the kernel would definitely remain the same, but the player software would be whatever was on the old secondary drive. This could be the same, an older version, or nothing. Either of the last two is pretty bad. Of course, the drives aren't going to magically swap on their own.

Also, after you've done the builder thing, the drives have no software on them. They've really just been partitioned in preparation for software (and music).