You probably created the emergency disk some time before you changed your CD-ROM setup. You always have to create a new emergency disk if you change your setup.
Now you must fix the disk by hand. You must know the name of the driver (e.g. scsi.device) and the unit number of the CD-ROM (the SCSI ID). Then open the CD0 file on your emergency disk with an editor and change DEVICE=whatever to DEVICE=yourdriver and UNIT=whatever to UNIT=yourscsiid. Note: it may well be that the CD-ROM moutfile on the emergency disk is not called CD0 but EMERGENCY_CD, so use this if you don't find CD0.
Of course to load an editor you must boot the Amiga. You should use a Workbench floppy as suggested before.
Bye,
Thomas