Perhaps I'm missing something obvious, but isn't this trivial to solve by just having a deduping filter at the lower level? When the higher level starts keeps sending duplicate packets, just ignore them. Duplicate packets at this layer will always be useless, because your lower layer is already implementing reliability semantics. Then, when you get ACKs from the other side, translate those packets to match the sequence numbers that the higher level is expecting (i.e. the most recent sequence number that was sent out corresponding to a packet with those contents).
