Your workflow can't work with Bookmarks and Ref fields. If the bookmarks exist on the first page, the ref fields are fine but as soon as you delete the cover page, the bookmarks no longer exist and the Ref fields will all break (when next updated).

This task should be done with linked content controls. This way, the values of each linked CC are stored in an embedded xml file. The cover can be stored as a building block and inserted in each doc and the values in each CC will reflect the values stored in the xml file (and hence be relative to the document where the CC is inserted).

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Andrew Lockton
Chrysalis Design, Melbourne Australia