I also posted the solution in another thread, sorry for the double entry but just to be comprehensive
In the end it was quit simple and the issue was in the ereader itself. AND I found a better solution for managing my books as well. I downloaded calibre to check if this helped. And yes, in a way. I could copy the book which caused the trouble but after i opened it on my ereader (worked), closed and try to open it again, the directory structure was a mess.
So I took the drastic approach and formatted the memory of my bebook. This helped and now it is working again. And sorry for ADE, calibre is a much nicer program which sees the SD card as well, gives more functionality and is much faster.
I hope this helps others, it was hard to find a solution on the internet
