vw_tagged and vw_bbcode are dropped after the upgrade to 4.0.6, and the point of these steps is just to copy the data from those tables somewhere else before that happens. So if they are already missing, then you have nothing to copy, and I suppose nothing to worry about.
It seems somehow you finished upgrading to 4.0.6 (maybe another day last week), but then went back today and tried to do it again. I am not even aware how that would be possible, since vw_upgradelog records what step you last completed and changes the step numbers so step 1 is always the next step that wasn't completed yet. Since you are the only user who has encountered this and otherwise 4.0.6 has been a smooth upgrade for people, I think the only thing we can really do is wrap these steps so they don't run if these tables are missing. This was something we noted about 4.0.4, so I'm surprised some steps in 4.0.6 were overlooked.
Otherwise, I see that it is possible to be missing vw_tagged on XenForo, but not vw_tagged and vw_bbcode at the same time unless the above is true (or they were manually removed). In order to be missing vw_tagged, you would have to have installed VaultWiki 4.0.0 Beta 3 or lower, and then have upgraded. It seems the step that creates vw_tagged in 4.0.0 Beta 4 was not successful in XenForo at the time.
I don't think you need to clean anything up, but check your XenForo BB-Codes, and make sure the VaultWiki-related ones have desirable "Wiki Options" settings.