I have a Da Vinci AiO that will restart and reinitialize during downloads of a big print. Simplify3D says it has lost communications at that time. I am running MacOS 10.11.1 and the firmware for the Da Vinci is 1.1.6.
I've seen some massive bugs with the firmware for my old da vinci. XYZ knew about the issue. In the early days, the uploads to the printer used to fail almost 50% of the time! Same thing happened with the stock software. I still happens now, but it's less frequent. For really large files, you may just have to try the upload a few times until it works. It stinks, but hopefully XYZ will keep working on their firmware to fix it. There has definitely been improvements from their last few firmware releases
Hmm. I'll give that a try, because I think I'm having the same problem. Unfortunately, I've never been by the printer when the "disconnect" happened, but that sure sounds like what is going on. Since I have not seen this from Simplify 3D on Windows (which uses the "\r\n" line endings), that might be a clue.