This is interesting, because the size of a file's encrypted chunks now leaks information about the file's plaintext. I suppose you have some minimum chunk size, and that's one way to keep from leaking too much information as a fraction of the overall file size. But if a file is modified many times, it seems to me that you'd have to be very careful not to leak a substantial amount of data to a clever attacker.

Have you thought about how to quantify this tradeoff?

I suppose you could pad each encrypted chunk so they're all the same size, but then if you don't want to waste a ton of space you'd have to restrict your chunking algorithm to output chunks with relatively similar sizes, at which point you lose some of the benefits of chunking.