Quote:
Originally Posted by RicciBobbi
Success! After converting all books to MOBI I then transferred them in batches using the send specific format option to make sure they all went across as MOBI files as a lot of them had multiple formats. After transferring all the books I ran the collections plug in, restarted the kindle and everything is set up perfectly! Thank goodness for that. 
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When adding a significant number of books at once (even if you did it in several back-to-back operations) to a Kindle makes it go into an indexing mode for a significant time, even when the Kindle is sleeping, and this tends to drain the battery quite quickly. Leave it plugged into a wall charger overnight (or depending on the amount of transferred books, several nights).