Premiere failing to export long video "file does not exist" error
Try doing it as a two-step process:


Export your movie with the identical format as your sequence, using a reasonable high-quality ProRes format as your output (so you don't suffer much the damage of double-compression)
Compress the output of Step 1 into the format and codec you like


Premiere Pro and Adobe Media Encoder have all kinds of problems right now, and not only with El Capitan.  Many others have hit the same glitch you have, both on Yosemite and El Capitan, with or without hardware rendering.  CC2015 has been a big disappointment to many.