Originally Posted by itimpi
A question I have been meaning to ask - are any issues likely to arise if I remove books from iBooks directly on the iPad after reading them rather than using Calibre to remove them? Just want to check that there will not be any unforseen side-effects with the metadata caching or anything like that
Revised response: It depends on how and when you remove the book.
If your iPad is connected
to your computer and calibre, use calibre to delete books on the iPad.
If your iPad is disconnected
from your computer and calibre, use iBooks to delete books on your iPad. The next time you connect, the driver compares the books currently on the device to the last known set, and removes any missing books in iTunes so they won't be re-added next time you sync.
I just reviewed the code that handles this and found a bug that will be fixed in 0.7.3. In the meantime, deleting from calibre will do the right thing.