I noticed after it happened about 5 times. You copy files (m4v, mkv, others) to your SDCard and after you reboot they are gone. This happens on Vegan as well as others I had read.
To keep this from happening, in the root of your SDCards (For me /mnt/sdcard and /mnt/sdcard2), create a DIRECTORY called .nomedia You cannot use Windows to do this, you must do it on a linux/unix machine or from iFilemanager,Astro or another file manager type application.
I haven't had trouble since.