Are you waiting long enough after you open a project for After Effects to do an auto save? After Effects creates an auto save after 20 minutes of working on the same project. Ae may not create the folder until it's time to make an auto save.
Without any system info and other details like what version of AE you are using and what the preference settings for the auto-save are we can't realyl tell you anything. You need to be much more specific.
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