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If you are willing to pay a different price - additionally to the current version keep also the last version locally, calculate, encrypt and upload the diff and later download the base version and all the diffs and apply the diffs after decrypting everything. This trades storage space on both sides and download volume for upload volume and it obviously heavily depends on the usage patter whether this is a good trade-off or not.

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I touched on this in an above comment[1] (after you posted so I didn't expect you to see it), but essentially because of how AES CBC[2] encryption works, an encrypted block relies on the previous block to correctly be decrypted. Uploading and replacing blocks that are different will not work; the next time that file is decrypted every block after the first newly uploaded one will not be correct.

[1] -- https://news.ycombinator.com/item?id=7787791

[2] -- http://en.wikipedia.org/wiki/Block_cipher_mode_of_operation#...

You could for example use ECB, OFB or CTR mode and actually update the file (some options are obviously a bad choice) but I thought of storing the file and the diff together and only apply the diff after decryption so there is no need to mess with the encrypted data in the first place.

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