As my sister began telling me about the scorpion in her bed that stung her as she slumbered, I could feel my eyes popping out of my head.
The two actions are taking place at the some time. They will be, usually, in the same tense.
"that stung her as she slumbered" is a relative clause. Its tense is not dependent upon other tenses - it is separate ...
We had become friends when nobody had liked him and it had seemed no one ever would.
There is a simple answer to your question.
Time, though is a tricky thing. It seems this novel has a narrator as one of its characters. So you are dealing with the following times.
The time at which the narrator is telling the story.
The time(s) in which the story or the ...
The sentence is flawed. Two corrections are needed: "cases" is plural and should not follow "an"; "fall" should be in the same tense as "related". I suggest it should read "Had this been related to an existing case, or had it fallen within the supported thresholds, we would have..."