If I understand my Linux-fu correctly, HDA and HDC are not drives. I think they are partitions within drives. I could be wrong about that, though, maybe they're the physical drives and drive0/drive1 are the logical drives within them. I forget. But I do know that the empeg has several partitions for various things.

But even more to the point...

There is an interesting trick they do to make the Mark2s and the Mark1s seem to have the same partitioning scheme. See, the Mark1 had two IDE headers so both drives were always primaries. The Mark2 has one IDE header with master and slave. So there's some trickery in the boot scheme that makes the partitions behave the same on both models, and I think the HDA/HDB/HDC naming scheme enters into it. Unfortunately I don't know the details of this.

In any case, if you swap drives, all the partitions and such move around to where the new drive is. They don't magically keep their names and positions. If you move the jumper, everything changes.

The disk upgrade guide has all the procedures you need to know in order to copy files and such between drives so that you can change the number of drives in the player. Just follow those steps and you'll be fine.