Deleted classes are still in the lookup drop-down, introducing confusion.

[turkhale]

[turkhale]

For example, some of these resources are deleted, but still, I can select them:

[turkhale]

I think the overall flow for deleting resources is unclear. Whether I delete the class or delete only this resource, I don't understand. Usually, in modeling, we say "delete from the model" (remove altogether) or "remove/delete this instance."

[turkhale]

Overall, the UI problem is that I see only some of what the model contains on the back panel. It is incorrect for modeling purposes (though perfectly fine for the end user).

[joepio]

I think the overall flow for deleting resources is unclear

I think you're right on this. I'm assuming you removed references to properties form the Edit page. You expected the linked resource to be removed here, but it keeps these around.

I think the solution here is to use the Ontology Editor, which does handle this correctly.