The scanner didn't have a prompt for safe removal. It only said not to remove while it was saving the file; I don't know if I waited 30 seconds after it was done saving.
I've done a windows PC disk check and am now stuck with a bunch of .chk files. I am sensing a reformat or a reflash in the near future.
P.S. There is nothing to backup from MyDocs, everything is gone.
This happened to me more than once on the N900 (I was just as scared first time it happened) and regular fsck always fixed it. I think I had done it using my Linux desktop I connected it to via USB, but trying fsck on the N900 as I type, it looks like it's available there as well (at least with KP 53).