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Something is missing in what you tell so far;
What event(s) happened before this??
Did someone move to another computer or try to rebuild / restore because some error message showed up?
Did 2 computers access this file (ANY kind of Network shares are a recipe for corruption. The content server is the only safe way for more than the 1 user access).
Calibre has extra files stored to help rebuild (NOT RE-add) that construct all the custom columns before proceeding. A simple ADD has no knowledge of those extras.
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