I think it is an other problem. You forgot to put a filesystem on the new HD in the HDToolbox. As long as the old internal HD is connected it is no problem, as the amiga will take the filesystem information from that drive and use it to read the "SCSI" HD. Once you remove the old drive the Amiga has no clue how to read from the new drive, it`s like there is not data on the new drive.
Open HDToolbox, see whet filesystem ist "assigned to the internal HD and put the same on the SCSI HD. As the new drive is already formated with this filesystem there should be no Problem or dataloss, but just in case make a backup before doing this.
An other issue could be that the bootpartition on the SCSI HD isn`t smaller then 2 GB
