How did you try to reorganise? Just attached it to your computer and moved them around?
One thing that comes to mind for fixing the error message is putting the SD card in a reader on your PC and do a file system check with whatever OS you have on your desktop. If that doesn't help, you could search the card for an XML file, it could be corrupted. If you delete it, your reader will rebuild the book index but you will definitely lose all bookmarks and other meta-information.
Regarding series, what I have found is that once you start to use series, you NEED to use Calibre to transfer the files - just schlepping them on using USB isn't going to get you the series, AFAIK. My solution so far has been to use title names with the series name and a number in the title, that way you can always find book X of series Y, whether you've screwed up the series or not. This might not work for the "purists"
The bookmarks might well be lost, I had that a couple of times before
