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I do stand to be corrected on this but as far as I have experienced if the sync.ffs_db file is deleted on either or both sides of the sync FFS will do a scan but will still only want to write across the files that are on the Compare side but are not on the Synchronize side, plus write new sync.ffs_db files - it will not want to write everything across as the OP experienced.
That does bring to mind trying deleting the sync.ffs_db files in the folders on both sides and seeing if that causes FFS after its scan to recognise the existence of the files already on the card and not want to write them again. Again, a long shot I would have thought.
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