It sounds like you ran across an error message that shouldn't have occurred (the real issue should have been caught before you saw that message), so I'll look at doing some additional checks.
Templates can be confusing, but there are step by step instructions I'll add to the first post once I can test them in the next version of Calibre.
For your new books, first make sure they have been sent to the device. If they aren't on the Kindle they'll be ignored by the plugin. As for making updates in Calibre that aren't seen without a restart (its the reconnection of the Kindle that does it), that's a limitation in the current plugin version. But I'm glad to say that will no longer be an issue in the next version since I'll use Calibre's library info directly instead of reading it from a copy on the Kindle.
Thanks for the feedback.
