Well, the subject.
SI copy/paste config state is reset to the default after ANY mod update.

I'll check if I can do something about it, I don't remember if I made it reset myself to avoid other potential bugs.

Copy and paste still seems broken.
Copy and paste from one Basic slim to the other changes the settings.

It's a different topic, the problem you're referring to is not the copy-paste configurator but the mod inner working, I guess you're the same guy on discord so I wrote just to clarify here.

According to API Docs, the exact data of what was changed is passed to the on_configuration_changed event.

This line creates an empty data table only if it's missing, when this function unconditionally resets the data.

My suggestion would be:
1. Game version change:
- Patch: Keep
- Major or minor: Drop
2. Mods list change:
- SI in the list: ?
- SI not present: Keep
3. Startup changes: Keep
4. Migrations applied: ?

So I will change the behavior to update only when something changes in SI/ YAFLA (maybe).
I'm working on something and I'm planning to make a full rewrite of some functions so this will take a bit.
The migration will always be a full reset to the base configuration of that version, having a migration for the actual content of that menu is probably unnecessary (I'll probably add a message in chat to notify the player).

Still, I was surprised (nicely) that you took the time to look at that awful code.
this function should not have changed the settings since the line that add checkboxes this should keep the data "state = global.SI_Storage[player_index].copy_settings[name]"

I guess I was missing something somewhere along the pipeline of the function ensure_data.

Sorry if the message is long/technical I don't get every day a chance to talk about this code so it was fun for me.