You'll need to do the eMMC first, then the main firmware. And yes, you'll lose the maps and all other data on the phone (including ringtones) when you flash it. You can try powering the phone off altogether and plugging it in via USB - this should mount it in mass storage mode, allowing you to copy anything you want off. As for reinstalling the maps, you can use the Nokia Map Loader to install/update the maps on the N900 (you need the 3.0.28.0 version, and there's some workarounds needed for Windows 7 and 64-bit Windows).