Firstly I'm not an SQLite expert but, now you know that, I would guess SQLite
marks deleted records waiting until some clean-up process removes them and
re-writes the active data. I would therefore look for some bit that is set.
Try setting up a new database, adding records - taking a copy, then deleting
the records and then compare the two images. That should point you to where
SQLIte is tagging records. Then you go back to your target database and
'unset' the deletion flags, now you know where SQL puts them. You should
then be able to see the deleted records again. 
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