As Kirk noted, The incremental ingest feature keeps track of what files were ingested off each individual card and will skip them on subsequent ingests -- even if you've deleted/moved them off the hard drive. Each card's record is separate, so if you ingest IMG_001, IMG_002, and IMG_003 from card 1, delete them and then plug in card 2 with the same files, they will ingest. This is how it was designed.
If you want to re-ingest files from a card that you have previously ingested and then deleted/moved the files, then turn off incremental ingest.
-Mick