Object deleting a sim by way of testingcheats only deletes their body. Their sim data remains in the game and can cause issues the next time that sim is called upon to do something. Repo sims are Service Sims and chances are NRaas mods if they are in play are stepping in to correct or expunge the remaining sim data at least sometimes; a repo sim is not likely to have much in the way of history or deep character development. But regardless a new one is going to spawn the next time one is needed anyway, so even deleting them a better way isn't really going to accomplish much long-term.
The white boxes usually pertain to objects that have dependencies that are missing or the objects are not fully installed themselves.
