If the data isn't H.264 data, then it should be placed in a custom SEI packet. You don't need to change the internals of the encoder for that, just the way you call them from lencod.c (probably by modifying the main loop in encode_sequence()) by adding the SEI after each frame. The SEI will be skipped by decoders that don't understand it, but available to those that do.
Isn't FEC usually done at the RTP level, though?
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