That's interesting because when I first hit the indexing problem it was after sending a lot (250+) books from Calibre. I always use "send to device". Subsequently I did a reset and then sent them 10 at a time and then later one at a time. I had thought about simply copying them using the OS and cutting out Calibre altogether (I don't really think it's an issue but I could remove the calibre created files).
My latest tactic is to try to download as many of the books from Amazon as possible and only sideload ones which originally came from other sources. This gives me a smaller set if I have to start weeding out "problem" books.