Starting with the disclaimer that I don't know a thing about HP large-format printers, the problem description sounds like a hard disk directory structure error - in which case, is there any reason why you couldn't just put in a properly formatted hard disk? Even if the directory structure is proprietary, you may find that a sector-level copy could be used to make a disk clone from a working disk.
Or again, I might be right off track - if this is the problem, I'd expect the HP tech folks to have just suggested a replacement drive, instead of the whole formatter, if it's at all possible to get the disk out.