IOS: Don't let Kernel initialize WiiRoot if already initialized

The SaveToSYSCONF call in BootManager.cpp was unintentionally
overriding the temporary NAND set by the preceding
InitializeWiiRoot call. Fixes
https://bugs.dolphin-emu.org/issues/12500.

Source/Core/Core/IOS/IOS.cpp

@@ -256,8 +256,11 @@ Kernel::Kernel()
   // Until the Wii root and NAND path stuff is entirely managed by IOS and made non-static,
   // using more than one IOS instance at a time is not supported.
   ASSERT(GetIOS() == nullptr);
-  Core::InitializeWiiRoot(false);
-  m_is_responsible_for_nand_root = true;
+
+  m_is_responsible_for_nand_root = !Core::WiiRootIsInitialized();
+  if (m_is_responsible_for_nand_root)
+    Core::InitializeWiiRoot(false);
+
   AddCoreDevices();
 }