What should one do who filmed his female neighbor with his phone three years ago, then repented, deleted the video, and regretted his action?

You have erred by secretly observing people's private parts while they were unaware, and by photographing women, especially if they were displaying their adornments. You must offer sincere repentance. The fundamental principle of such repentance is to seek forgiveness from those whose rights you have violated. However, if you fear that doing so would cause greater harm, then supplicate for them and seek forgiveness for them instead.