I own a T3 but I don't let calibre do anything with it. I load my books via Windows Explorer, then let the eReader do its job.
My decades long experience with all kind of devices with storage is that it's always, always, always better to let them organize their content. They know better. I know cases where people tried to copy/delete SAT-recordings via computers, in the end they managed to delete the logical pointer to the data, which remained on HDD without being accesible - the only way to recover the lost space was a re-format ha ha ha. Minidisc owners (NetMD) can join this choir.
If you have such a huge library that you cannot manage yourself, do you think you'll have to time to actually read it?