How to Check If File is Encrypted using AES (Rijndael)

Without any sort of custom headers, the only way to be absolutely sure the file is encrypted is to attempt to decrypt it.

If you attempt to compress the file and it gets smaller, then it is extremely unlikely to be encrypted. If there is a non-uniform distribution of byte values (including plain text!), then it is unlikely to be encrypted.

Those heuristics depend on proper execution of the encryption. If AES is applied to a file one block at time, then patters can emerge in the result, but since you are using CryptoStream this shouldn't be a problem.

If your own code will always be used to encrypt and decrypt the files, then you should consider adding a custom header that indicates it is an encrypted file.

Suppose I have a file F containing ciphertext X, which is the enciphering of plaintext Y with key Z.

I wish to ensure that the plaintext Y can only be determined by someone who possesses both key Z and key Q. (I can think of a number of reasons why I might wish to do this.)

I therefore wish to encrypt the already-encrypted file with key Q.

You're telling me that your system wishes to detect that F is already encrypted, and then refuse to encrypt it with key Q?

That seems like a bad idea. I might want to encrypt the file with key Q irrespective of whether it is already encrypted with key Z or not.