I disagree. You can deterministically chunk the large file with one of the existing rolling checksum schemes, and then use the chunks as your primitive instead of whole files. The server only sees encrypted chunks. The client knows to only upload changed chunks.
That still leaves important choices to be made about cipher mode, key management, etc. But it's not intractable.
My understanding is that CBC is among the most secure forms of AES encryption because it is essentially impossible to have patterns in data (unlike EBC). Practically speaking then one must assume that it is common to upload most of a file. Any software that boasts this security cannot effectively 'diff' your files.
EDIT: Formatting
If you manage to merge small files into the same blocks, you even gain some privacy because the server can't even tell the number of files anymore.
[1] also has a discussion of the trade-offs of the different modes of operation for whole disk encryption. That seems related here because nobody wants to rewrite the whole disk after changing the first byte.