When breaking a controller, the insert/sort upgrades are gone, and so are the materials used for it. Ideally the controller should also drop those items if it has those upgrades.

I'm happy to work on a PR for this if you'd like to assign it to me.

This is actually intended "it's a feature". There are not a lot of resource sinks. So, there is a little cost for repositioning. The upgrade is done on left click.

Oh? Okay, if this is intentional, I'll close the issue.

If you're interested you could drop some "left over resources" of the upgrade to make this more clear (3 redstone dust, a chest and an iron ingot) or so.