I've never done exactly that but do you unmount the drive before removing it?
Code:
umount /dev/cdrom or whatever it is mounted as
Then after installing the other drive do you mount it?
Code:
mount /dev/hdc /whatever/directory/you/have
I think you will have to be rather specific during the mount or make sure that the fstab file is correct for the drive. On my laptop with FC2 the entry for the cdrom is /dev/cdrom so I suppose that I could make another entry for an hdc.
I have a spare drive and was thinking of getting the parts to use it in the removable bay and am interested in your results.
Even in Windows you are required to unmount the drive before swapping it with another. The proper Windows term for the action escapes me at the moment.