if there are var, cus,usr layer in ax system, and modify object in var layer and usr layer, the code will keep var layer code until you modify it in usr layer. and then whatever you modify it in var layer or usr layer, the code is saved in usr layer.
if you want to migrate the code from usr layer to var layer, you should find all object modified in usr layer and put them into a project in usr layer, and export the project. and then delete the code in usr layer. finally you import the project in var layer and do some checking after importing..