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When the Libraries have Pages inside of Folders on the PAS Server, the tool errors and dies. The fix would be to support recursively going through the folder to find the guids and do the matching.
Due to the recursive nature of folders, the existing structure of Library / Book / Page will be used when mapping with the Excel lookup file, and will be used for PPS (still works fine!) to keep it simple and always 3 levels - the folder will simply be ignored.