Do you have a save state from this playthrough from before you got to Stineford that you can go back to and replay to see if you can get it to recur?
There's a literal 1 in 100 billion chance that the bit containing the "SeenTunnels" switch got turned on by looking at the hole, along with the self switch that's giving you the "..." response, and then got overwritten to off in a copying error or a random X-Ray hitting that exact spot on your RAM or HD.
That's the switch that should trigger Yarra's dialogue on the tunnels being hidden by illusion in the inn.
Alternately upload your save and hopefully Fulminato will look at it.