I'm not sure, but this might happen every time XenForo is upgraded. It could be related to XenForo disabling all code event listeners during its upgrade process, so if it performs a rebuild of the BB-Code tag cache, the VaultWiki-related info won't be included in that rebuild. I could be wrong about this, but that is the first place I'm going to look. In that case, we'll probably have to force a cache rebuild on-demand if the tag keys are ever missing.
If XenForo does rebuilds while add-ons are temporarily disabled, I suppose this could cause other issues, such as problems with wiki styles after the XenForo upgrade.