If you want to upgrade from a previous version to Recycling 4.0:

- clean up the old stuff first
- deactivate the old mod
- save your map
- enable Recycling 4.0
- load your prison and start placing the fresh objects.

You could disable the old mod without dumping old stuff up first, but this will result in a lot of boxes/stacks called "None" in your prison.
You can clean that up with my DevTools mod if you wish (using the Remove None tool).