Well, moving everything in that directory to another disk in that way are probably a very bad idea. Besides ibays, there are some other things that belongs to the system itself and it's likely that it will break something.
HowTo:
It's intended for special purposes only where you can benefit from mounting a dedicated harddrive to an ibay.
I'm not shure of what you want to achieve but I suppose you wanted to move your whole content to another harddrive. If so, I think this would be a better approach:
1. Make a complete backup using "Backup to LAN workstation" and then verify the backup to be shure.
2. Reinstall your server with the new hdd(-s) in place, and configure backup details.
3. Restore the old content from the backup.
But, in your case with a server that's already broken, you have to restore from an old backup.
If that's not available, I would pull out the new harddrive, mount it in another computer (or USB-box) and try to save whats left to be saved.
I know it's not answering your question about symlinks, but I think you are out in deep water if you go any further in that direction (and well beyond my knowledge).