The situation you describe is very unspecific.
What is long time.. What is "many files" in it.. 100 ? 1000 ? 10000 ? 3 Million ?
When the zip files is deleted, MC will cleanup its internal representation of it. And if your browsed into it. All of that are cached, So if it is millions of objects that should be cleanedup, it can take a little bit of time.
