I understand that but the very same emails that were sitting in my inbox on my laptop are the exact emails that are showing on my phone in aquamail. Doesn't seem possible but that is what i see. I always move emails in my laptop into folders to save them. Never take anything off server. And the laptop and phone are synced.
If my clock is synchronized with the atomic clock at NIST in Colorado, and your clock is synchronized with the same atomic clock at NIST, your clock and mine will show the same time. But from this, it doesn't follow that our clocks develop telepathic ability to synchronize to each other.
The same happens with the e-mail. The folder structure that you see on your phone and your laptop under your e-mail account (if you are using IMAP, EWS, or Activesync protocols) lives on the server. And that's the reason while you see the same folders and messages in them on all your devices.
Moreover, while on your laptop you can create "local" folders (i.e. those that exist on the laptop only), -- on the phone, in Aquamail and many other e-mail apps, there are no "local" folders. (Strictly speaking, there is a possible exception of 1-2 folders with special functions, such as "Sent" or "Deleted", - and only if one purposely "decouples" them from the folders on the server).
I hope this helps...