When using miniloader with K2 mod, the advance miniloaders will not upgrade to superior miniloader with the generic upgrade tool.

I was advised the entities flag is set wrong.

Yes, can't upgrade from K2 loader to miniloader and vice-versa. It's sad because I need to upgrade my whole base manually...
Upgrade planner mod doesn't work either.

Also, the replacement of loaders from K2 does not work. It's annoying and frustrating, especially when you don't know whose fault it is. I think the developer can make some kind of exception so that both types of loaders can work together.

Upgrade Planner might be able to support this, but I expect it'll be hard. K2 loaders are loaders, while Miniloaders are inserters with funny graphics. As far as the base game is concerned, you're trying to upgrade a loader to a stack inserter, which it doesn't support.