I asume you bought one at weltbild.de, which is NOT able to use MOBI/PRC format, but can use ePUB instead. This is clearly stated on the weppage, but we here at the forums already discussed about people having problems with these "new" CyBooks...
So your reader was perfectly OK until you tried to repair the internal memory. Problem is, as there is no new firmware version downloadable at the moment (not ready yet and weltbild.de-release was a special version) it'll be hard to restore the thing (without Bookeen support).
Maybe this thread here is of some help (later posts):
CLICK
When Bookeen finishes the new firmware version there'll be hopefully a version that supports ePUB and MOBI/PRC formats!!!