Don't panic, don't do anything rash. MyDocs might not have gotten remounted by the phone if the scanner wasn't playing nice. If that happened, you'll just see what's in an Actual MyDocs directory -- which could have stuff that got saved there when MyDocs was mounted by another host some other time -- rather than the partition that's usually mounted over it. It'll look like everything's gone when it isn't. Try remounting MyDocs or just restart the N900.

If the worst happens as pichlo hypothesizes, you can use photorec and testdisk on the dd copy of the partition. You can probably even use "ddrescue" instead of "dd" if you've got a Linux desktop handy, it's more robust and can skip over (and even retry) bad blocks.

But first, don't panic.