I was wondering whether anyone else has experienced the following - and if not let this be a warning
I attempted to transfer 4 files to the reader. However, there was only room on the reader for 2 of the files. After transferring the 2 files, I found that all my collections were gone. The books themselves were still there, so all I needed to do was recreate them (somewhat of a pain).
Apparently, when it was trying to write the 3rd file for which there was not enough memory it must have overwritten the collections in the internal memory.