I don't use the sheet production tools so I am not sure how it sets up the references but I suspect it uses the level display settings that were in effect when you cut the sheets and the references are attached with the Override option set to Never. See screen cap). The reason for that setting is to allow you to control the level display in ALL the sheets simply by turning them on or off in the source file(s) that are referenced into the sheets. So you should figure out which files are referenced into the sheets and open those files and make sure the contour levels are on.
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