There was good news and bad news.
The good thing was: the organization no longer existed. The bad: No remaining research documents on the Aptx 4869 either.
Thus, Ai had neither the possibility to return to their earlier sizes nor the shrunken Shinichi.
The detective thus had two options: Either he would continue to play his role as Conan or he would necessarily tell Ran the truth.
He chose the latter.
He told her, which, to his astonishment, she received quite calmly.
When she told Sonoko about it a little later, she laughed at her friend's boyfriend.