I mentioned this on the Grail Github when posting about the 10.0.7 .toc issue, but it occurred to me this might actually be more of a Wholly issue, than a Grail one.

Link to a screenshot in that issue: smaitch/Grail#335 (comment)

I mentioned earlier in that thread that if one uses the Search command, the missing quests can often be found, but the do not show up in the interface under their zones.