I am running small Kareha board. Somehow one thread got disappeared I don't know how. Limits are disabled (manually of by default) or set to other values, so threads shouldn't be autodeleted, I think.
There were 5 pages, and that thread was on 0 page (though it was old, but most active, post limit and bump limit was not reached). OP didn't deleted it too. Where could be the problem?
Also, TRIM_METHOD is better to set to 1? Maybe because of this that thread was gone.