Your description is a little vague. But it sounds like you are loading your changed plugin with the same savegame. This is likely to cause problems of disappearing and doubled items due to the Construction Set renumbering reference numbers when you make changes in a cell, sometimes called the localref problem. The solution is to start a new game after you have made any changes to a cell. You can verify if this is the problem by starting a brand new game, using coc to visit your cell and checking to see if everything is ok. If it is when you start a new game, but things are missing or doubled when you use your plugin with a saved game, then I think it's the localref problem.