This is by design. Tags should not be duplicated between IFD0 and the ExifIFD, so ExifTool takes care of this by deleting the tag in the other directory when you write it. If you really want the value in both directories, you must write both of them at the same time. In general, it is best to just specify EXIF instead of IFD0 or ExifIFD when writing because then ExifTool will put it in the proper directory according to the EXIF specification (although I have seen tags often enough in the wrong directory -- this is part of the reason for the logic to delete them from the wrong directory when writing).

- Phil