Items required in the settlement cannot be duped. You can dupe them, but it'll just return to the original amount after relaunching the game. Even if you pay real money to get materials in your inbox, when you claim them from your inbox, only the amount you paid for would stay (sometimes those disappear, too!). Some of these items are Sheaves, screws, sawdust, asbestos, iron wire, rubber hose, antenna, resin, motor oil, spark plug, rubber hose, light parts, iron parts, iron pipe, all types of frames, all types of billets, all types of beams, chipboard, iron rod, coil, rotor, aluminum cable.
If you messed up and duped them so many times that you ended up with a negative value, try to find one of the items, dupe them to the exact negative amount, and fill it in. So let's say you're sitting at -1699699 iron wires, so find one iron wire and dupe it to the nearest amount, then turn it in and when the value becomes positive or 0, leave the game and relaunch (this is how I fixed it).