Download the new zip and copy its files over the same AutoApply folder you loaded before. Then open chrome://extensions and click the reload icon on the Auto Apply card.
Load it from the same folder path. If you load it from a new location, Chrome treats it as a different extension and your saved profile and answers will not carry over on their own.
From v0.9.0 you do not have to re-enter anything. Sign in here, open Profile and press Connect my extension. Your profile, saved answers, resumes and tracked jobs are stored on your account and come back, even into a fresh install.