Readynas ultra 6, dead drive stills shows as working in raidar? And not expanding

I would test the drive with the manufacturer's tools (such as Seatools for Seagate, though it works well on most others, too) before replacing the drive.  Your mixed signals on whether the drive is dead or not can happen due to other reasons.  I believe mine did it because of one brand being slower to spin up than another.  Once the system declares a drive "dead" it won't undo that unless you pull and re-insert it, even though it may continue to use it (I had two "dead" drives but my data was intact).  Even if it's not really dead and the problem clears by removing and re-inserting, once that chain of events has started, it may become necessary to factory default to stop the process from happening again (at least, it was for me).

Do not just try removing and re-inserting the drive unless you have tested it and have good reason to believe the drive is actually fine, like it passing using the manufacturer's tools.  The strain of trying to re-sync to a bad drive can cause other problems if other drives are close to failure.  You could try the built-in drive test, but it's a lot longer and gives less feedback.  Note that the removal and replacement (with new or same drive) is best done with power on, as the unit will see the drive removal and then insertion as separate events.

OS6 does not seem to suffer from this problem (at least not that I've ever seen reported or observed myself), and you definately want to consider it if you are going to do a factory default anyway.  There are a lot of reasons to make the change, a more recent version of Linux being high among them.  But if you are runing any apps, make sure they are available for OS6 before you commit.  Generally, there are more (and more up to date) apps for OS6 than OS4.2.x, but that's not always the case.  ReadyNAS Remote is also replaced with ReadyCloud, so make sure that meets your needs if you use remote access.  If you have other NASes, keep in mind that ReadyCloud and ReadyNAS remote clients cannot both reside on a PC.

The order of the drives doesn't matter.  The screen on the front of the NAS keeps the airflow constant rather than it relying on resistance from the drives.  They may run a bit cooler if you leave the middle slots open, though.