Are you updating from the global minutely diffs? If yes, while I don't know the exact workings of nominatim, in general this will cause additional objects to be added outside of the area of your original extract. There are numerous ways around this problem, one is to consume diffs that are specific to your region as, for example, provided by GeoFabrik http://download.geofabrik.de/europe/netherlands-updates/

Are you updating from the global minutely diffs? If yes, while I don't know the exact workings of nominatim, in general this will cause additional objects to be added outside of the area of your original extract. There are numerous ways around this problem, one is to consume diffs that are specific to your region as, for example, provided by GeoFabrik http://download.geofabrik.de/europe/netherlands-updates/