The .system folder never disappears. It is hidden just like catymag says. Before you install SP and you have the files
on your PC, you can see the .system folder just fine if you are set to show hidden/operating system files (one of those 2). But after you install SP and you connect your phone to your PC the .system folder
on your phone does not show anymore, even if you still have hidden files shown. But it is still there. For some reason Windows Explorer can't see it. Might be if your phone connects as a media device instead of a mass storage device like my Samsung Note I717 does. To see the .system folder I use a third party browser, "MyPhoneExplorer" and it allows me to see all hidden files on my phone.
Your maps are definitely not moved into internal memory. Use a file explorer on your phone set to show hidden files and you can see that it is there where it always was. Check out pic. You can see in the notification bar that SP is running at this moment. I use Root Explorer.
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