You can find your save games in the following location:

• Windows: %LocalAppdata%Low\Double Dagger Studio\Little Kitty, Big City\
  
• Linux: <SteamLibrary>/steamapps/compatdata/1177980/pfx/

The format appears to be a modified JSON, allowing for complex objects and arrays as keys. Personally I recommend using Visual Studio Code or similar to edit the file.

Open the save game in Visual Studio Code, and change it to JSON format by clicking the "Plain Text" text in the bottom right corner and selecting JSON. Then right click into the document itself, and select Format Document, as this will significantly ease the workflow later on. Then all it comes down to is finding and deleting the area for the 4 special Rubber Duckies:

• c1cf3126-a106-4ec8-b973-102d9496f475 Bridge Duck
  
• 812ce296-dfa9-4240-8ac4-b01cafc2eab9 Patio Duck
  
• 84735315-7ee3-4a9a-89d8-c61d4b6614e0 Pond Duck
  
• 3e3d0ade-0920-49cb-8820-ab5514e20847 Store Manager Duck

While we can modify everything about the duck, we really only care about the ducks being in the right place. In the save game, you now want to search for the duck you believe to be missing, then select everything from the comma before, to just until the comma after the } block. See below for an example:


Once you've selected this, you can simply delete it, and repeat for every duck that you think is missing. Then save the file, start the game, and hunt the ducks down again. Alternatively, if you change the position of the duckies to you should instantly finish the achievement.