Blurb Book in Lightroom 5 on my Mac disappeared after 3 days of work. Where can I find a backed up copy via Time Machine or anywhere else?

Welcome to the WD Community.
1) I assume I can just hook the unit up via USB to my Mac and use iPartiion to reformat the drives, assuming each of the 4T drives will be seen by iPartition as a separate drive. That much seems straighforward.
Yes, and in case you ipartition dont see the unit properly, you can use the disk utilities on your Mac and you will be able to reformat the unit to make it compatible with your system.
2) Is my next step to reinstall the WD software and how do I do that? I've downloaded the Drive Utilities and Securities install apps - I assume I just run these with the drive still connected and that's all I need to do?
Yes, just run the applications.
3) What about the firmware update for Mac - when should I run that??
Normally, firmware updates are released to fix any issues that you might encounter on the drive. the latest one was released on 9/24/2014 and it fixed an issue with the drive dropping off of the list after system wakes up from standby mode.
5) And what about the "My Book Live Duo Setup" app for Mac - is that for a completely different model? What's the difference between "My Book Live Duo" and "My Book Duo"? It's these little things that I find so confusing.
Those are different units. The MBL Duo is a NAS (Network attached system) and the My Book Duo is a DAS (Direct attached system)
6) Lastly, when I have all the software installed, is that when I follow the procedure described in the Knowledge Base article ID 5724, "How to install a My Book Live or My Book Live Duo on Windows (8, 7, Vista, or XP) or Mac OSX for the first time"? Or is that procedure only for "My Book Live Duo" but not for "My Book Duo"??
That procedure is for the network units, not for your drive.

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