It is possible that you accidentally tapped a corner waypoint during the blue line verification step and overrode the current restarting point.
Our Manual Restarting Point feature is there so you can dictate where to restart.
1. If you interrupt the flight to fly manually there is a warning that tells you to put it back in programmed flight mode when landing so everything stays synchronized. Even this isn't always perfect so it is best to let the aircraft do its thing and not interrupt if possible.
2. If the duplicates you are talking about are just the images from the passes that were reflown it would be fine to omit one set of them or upload them. Uploading them all costs more points.