If use use AES-CTR you can decrypt any arbitrary 16-byte block of data from the file as long as you know its offset from the beginning. You don't need to know any other data of the file. As long as you don't need to insert or shift parts of the file without re-encrypting, this works fine. And you have to be OK with the file being padded at the end to a multiple of 16 bytes long.

Every time you want to read some data off flash, you read it then immediately decrypt it. Any time you want to write data to flash, you decrypt it first. Checking chapter markers or frame counts will be the same as before as long as you decrypt those bytes immediately after reading them from flash.