So, I haven't found a way to reproduce this, but I figured I'd report it anyway. I received a "could not connect to server" while attempting to warp to another sector, the serverlog is attached. After trying multiple times to reload the game, I closed it. I noticed that AvorionServer.exe was still running in the background (and was preventing Steam from relaunching the game), so I force-closed it. At that point I relaunched the game and I was able to load back in, but whenever I did so my ship had completely disappeared without a trace and I was in a random sector that was NOT my home sector.
serverlog_Thu_Jan_26_20-52-46_2017.txt