The metadata partition, the databases, and config.ini are on the first drive only.

My strategy for replacing my secondary drive was to build my new drive in the primary positon, then add my old drive as secondary (i.e. where it was originally), copy /drive1/* to /drive0, then remove both drives, and jumper the new drive as secondary, placing it with my original primary drive where it was originally.

Using two machines for this meant I didn't actually have to move my primary drive or reinstall the player and Hijack, but the principles should be obvious.