I tend to suspect the worst - that a rogue mod is arbitrarily deleting threads.
An example is the classic obit of Father Fahey, Card Counter for God - it still shows in the site search, but its gone -
Google cache indicator
There are more, but this is an example.
Ken, unless it was you, you might want to check the log or trash or whatever the vB system to see whether your massive archive is being subjected to abuse and who the culprit is. zg