1. If you are using a Time Machine backup, it backs up volumes and partitions, not specific users, unless such exclusions are explicitly placed in TM Options.
2. WD has client software that does try to mimic TM, but if encryption is enabled, the same utility from WD should be allowed and used to restore files. WD utility may have additional features like per user backups, which TM does not explicitly have. I would not touch the WD backup, because it is the only one that has the potential of a clean restore using what WD provides. I will research the WD software, because I do not use it and am a bit circumspect about TP software in general.
3. It is likely that the prepare phase on WD was doing a "full" rather than an incremental backup because it lost context when OS was reinstalled. The WD should maintain a synced catalog on both the internal and external drive, but software short cuts undermine such applications. It may also be doing encryption-during-backup, which will slow it down further, but that is research I need to do. If you have WD documentation check if it uses per file encryption or a higher granularity of encryption like partition level or disk level. It may be possible to unencrypted it, as necessary, later.
4. Since the Toshiba was erased (and is unlikely to be used to try and accomplish a "forensic" recovery), I suggest using the Toshiba as a "play" drive, not the WD.
5. I would recommend testing a small backup on the Toshiba. If you have another Mac, it may be worth it to test a small backup on the second mac/Toshiba to ensure that the Toshiba is not failing. Since you mention a good deal, I assume it is a "new" unused drive which no one else had hammered into submission.
