Make sure your feature definition file has a unique feature guid and don't let that feature guid change. If it does not have one defined in the file then it would get an autogenerated one so it would be different every time.

Setup isn't going to remove settings that no longer exist in the definition file, you would have to do that with a sql script.

Setup also does not create duplicate settings with the same feature guid so you should look in the database make sure the feature instance has the correct feature guid and that there are not more than one copy of your feature definition.