@BelgarionNL - I don't see this plugin won't be changing to cater for such an extremely rare (and silly) thing to do
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I explained above the reasons why the plugin does not auto-delete book records. It would have to compare every single field and custom column of the book record, and compare image contents to be 100% sure that two records are identical, it is such a minor edge case I cannot be bothered trying to write the code for it. Any thing less than that strict, and deleting becomes an arbitrary decision which may result in someone losing their perfect retail ePub copy and being left with some corrupted calibre conversion or whatever. It is not a responsibility I have any intention of taking any possibility of blame for.
As I mentioned several times on the original development thread for this plugin I always envisaged there would perhaps be one day a more intelligent "Smart Merge" plugin that would partner this one. So having identified the duplicates, you can use Smart Merge to help figure out how to resolve them and do auto-merging where safe etc. But no-one has written it yet, and it isn't on my todo list in the forseeable future either. By being more intelligent with your workflow of adding books to your library you can minimise the likelihood of duplicates occurring in the first place, and then just periodically scan with this plugin to catch any failures in that process.