I don't know if this relates to how you were working but it looks like books with DRM restrict how much clipping (and highlighting) you can do. From a previous post of mine.
Here's an interesting post
I read recently about the limit for text clipping.
I know there is a limit ,but not sure how much. Here is an old posting from a reader about clippings:
I did a test with a DRM'd Amazon book and a non-DRM'd book.
Using text size 1, with the Amazon book I was able to clip 39 pages. I got the error on the 40th page.
Using text size 1, with a non-DRM'd book, I clipped 80 pages with no problem. My fingers got tired so I quit, but I think you can draw your own conclusions. I did this AFTER the first test, so the limit is not in the myclippings.txt file itself. All the clips from both tests were in there.
Were you clipping a lot of pages along with typing notes?