Keep us up to date on your progress if you could. I found that the nook crashed after 1275 titles and there was a hack for a new library that fixed this. I would LOVE to know the upper limit of the Kindle. Also, at least a few Kindle tech support people have told me that the Kindle does much better and is faster with fewer titles in sub-directories. This is the way Calibre sets things up by default and is counter intuitive to what one would expect.
So, if you could (much appreciated) let up know what you find as the upper limit. I have close to 1700 titles from ManyBooks and here and it is very tempting to make the move. I just would hate to go through the 48 hours or so it will take only to find I need to undo it.
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