That's odd. I can unplug the empeg leaving the emplode session open, do some work, remember I wanted to make sime changes, plug the empeg back in and sync to it no problem. Even having the emplode session open for a long time while connected doesn't seem to affect it.
What are you using to connect? USB, network or serial.
Could there be some timeout setting?

Murray 06000047
Just increasing my post count