No.
The CFI table is accessed upon device initialization only. The fact that the flash programmer can't read it means that you likely have a hardware (board, SOPC Builder, or connectivity) issue.
Have you notified Terasic of this issue? If not, why don't you try that path in parallel with whatever sort of debug you're doing? Are you using an unadulterated example from them? If not, then I would make
darned sure that you've done exactly what they did in their example!
I've not used this board, or I'd have more advice for you....sorry.
Good luck!
- slacker