Originally the Kindle had no directory (a.k.a. "folder") capability, so all files ended up in one place, so obviously you could not have two of the same name.
This was OK for e-books which are PDFs with built-in tags and the thing built an index from the tags.
But for approach plates, you need to sort by country/airport so need 3 levels of directories.
The new Kindle does support them somehow, but nobody knows how. I think people who use it just use it for e-books and don't need to understand the issue.
Is there some sort of USB- or WIFI-connected drag/drop functionality?
I think the FLASH is 4GB which is far too much for transfer via the GPRS/3G feature, which is in any case charged for except when uploading purchased e-books. God knows how much they charge for it when you go abroad (roaming).
I had a play with the small Kindle today and it was suprisingly quick - much quicker to redraw the pages than previous e-book readers like the Irex. The DX version (necessary for the over-50

) looks quite usable for Jepp plates at approx 1:1.