Its a stange one as Lightroom doesn't "save" in the traditional sense. Edits update a database (the catalogue) and therefore when they are written to the database the are already "saved". If LR crashes it shouldn't overwite any data already stored in the catalogue. Therefore when you restart the database still has all of your edits and knows where all of your files are.
It sounds to me like the database (catalogue) became corupted and therefore reverted to an earlier version, maybe a backup copy. This copy must have been created after you improted the photos in question but before you deleted any of the rejects. Therefore the catalogue still though the rejects were in the original folder. Infact those originals had been deleted from that location.
It is definately nothing to do with XMP sidecars, emptying the trash etc. Lightroom simply doesn't work that way.
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Fletch
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Olympus E510 - Ok to edit and re-post on DPS only
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