This is listed as a known issue #1888869 (the first issue listed under "Known Issues with cross-references in InDesign CS4): the cross-reference panel won't reset in the hyperlinks panel. The issue is that the cross-reference window is all the way at the top of the panel; the grabber hand won't move it (solution #1); solution #2 doesnt' seem to apply to this issue. I am using CS6, so apparently this bug was never addressed. Help please!
I'm not sure what you mean by reset here. Can you provide more details?
Peter, thanks for responding. The issue was that the "cross reference" part of the window (usually the bottom 1/3 of the panel) got inadvertently dragged to the top of the panel, so that the "hyperlinks" section was no longer visible. The "help" for this was to click+hold on the horizontal bar under "Cross Reference" so that it changed to a grabber hand (this part worked), but the grabber hand couldn't move the horizontal line back down so that the "hyperlinks" section would reappear.
I finally fixed it by reseting the panel with the extension manager (didn't know the extensions manager existed): quitting ID, turning the hyperlinks panel off in Extensions Manager, restarting and quitting ID, turning the hyperlinks panel back on in EM, and restarting ID.