I have a same problem, sequence 1 have no audio problem when i send to encore using dynamic link but when i send the sequence 2, there is no audio/sound on encore (preview).
I play around and what i did is, i copy n paste the sequence 1 (which is no audio problem)- delete the video & audio and put all the content on the sequence 2 into the copy of sequence 1 and there is no more problem with audio when i send it to encore using dynamic link.