Something I've been trying to get you to understand - almost from jumpstreet.
You appear to have more than one problem - the error message you show comes from the so called magic numbers,which hold the serial numbers of the drives, being incorrect - and as you have already seen, this can be fixed by flashing the firmware.
YOU are a part of what's causing this, when you swap multiple drives in and out - you reset it without drives, installed an old drive, and then reinstalled the new pair of drives - the unit is not intended to be used like this and does not react well when drives are constantly swapped in and out.
You may have a second problem, a corrupt directory structure, and it's not inconceivable that your swapping drives in and out could be the cause of that, but I wouldn't go so far as say that it is. The file system tools required to fix a defective file system are not available on this device, and yes, I agree they should be, but without them, what's next? How long are you going to wait?
IF you have a corrupt file system, a reformat WILL fix it, a reformat will also fix the magic number issue.
Speaking from a background of 30+ years in IT support, which includes working on disks at a level that most people will never experience - we actually repaired the drives, replacing heads, platters, amplifier cards, etc. - there are some problems for which the only fix is a reformat, and there are others for which the quickest fix is a reformat.