Just to be clear, it will only save layers if you have layers in your document currently.
If you are reopening a flattened document, it wont recreate the lost layers.
If you do have layers when saving and then none when you reopen - have you tried resetting your Photoshop Preferences?
https://helpx.adobe.com/photoshop/using/preferences.html
In the new version of Photoshop you can save direct to the cloud
https://helpx.adobe.com/photoshop/using/cloud-documents-faq.html
or in previous versions you can use the CC desktop app to sync to a Creative Cloud folder.
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