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You won't get fragmentation of the Kindle's memory as such - at least, not that you can fix using defrag from a PC. The general opinion is don't try! http://www.mobileread.com/forums/showthread.php?t=104923skieblue said:And as far as the memory issue, I'll see if I can at least run an analysis on it the next time it's plugged into the computer and see if it's fragmented.
Thanks for all your help.

What you will get is that the indexes contain a lot of entries for books you've deleted and are therefore un-necessarily large.
If you remove a lot of books, it's a good idea to clear out the indexes before you add more books back on. There are instructions (from Amazon) here: http://www.amazon.com/CS-Dont-defrag-reindex/forum/FxBVKST06PWP9B/Tx20MFZ9YH0NAOX/1?_encoding=UTF8&asin=B000FI73MA.
Even if you've already copied all the books on, you could carry out the reindexing steps again. It will take a while to do, and will eat the battery, but the Kindle should hopefully be faster afterwards.