Partial encryption of a file? I want to partially encrypt a large block of data using AES. Meaning: given plaintext[0:1100], I would like to encrypt plaintext[0:1023]. The plaintext is generally machine code, but might have snippets of text. 

Does this expose what I encrypted to any realistic challenges in the context of my application (for example: copy protection)?
No, it doesn't have to expose information. Of course, any data in the last part of the file can be used to deduct information about the encrypted plaintext. Furthermore, it seems you want to perform in-place encryption. That's fine, but ciphers generally require an IV to make sure that the ciphertext is random even on identical plaintext. Using an IV generally means expanding the ciphertext size compared to the plaintext size.

There is one mode of operation that is perfect for encryption like this: CTR or counter mode (it may have even different names in other libraries). Here a counter is encrypted, and the resulting block is part of the key stream. You can simply XOR that key stream with the plaintext at the same offset to create the ciphertext. There is one big "but" (yo' mamma): CTR mode is completely unsafe if the counter is ever repeated, and the initial counter value is the IV. So you do need to store the IV somewhere where it can be related to the ciphertext. Possibilities are storage at the beginning or end of the file or in the meta-data of the (modern) file system.

It is also possible to calculate the IV, e.g. by performing a SHA-256 of the full path of the file name, and then taking the leftmost 128 bits. But note that any movement of the file will lead to corrupted plaintext (and possibly no way to decrypt if the path cannot be reconstructed). 



If copy protection is used then leaving part of the file encrypted may indeed destroy the copy protection, if the bytes are taken into account e.g. for signature generation, using a hash over the encrypted data. However, without more info about copy protection (which comes in many forms) then we cannot tell for sure. Of course if you can fully restore the file before copyright protection takes place I presume you are secure.