I've been having these problems for months now while watching Fractal do NOTHING. This is a show stopper problem and product runing problem for Mac Axe FX II users. It needs to be fixed now.
A few weeks ago Fractal support told me this is a bug in OSX. Apple promised to fix in a softweare update "soon."
What Mac and OS are you using? It might be helpful for some to know. I haven't determined I have a problem yet though. I've only tried Axe-Edit. When I reamp I haven't done it with USB. Maybe those who so and can't reliably do so, should merely do a workaround until it's fixed. I reamp a lot, but not the new USB Fractal way.
Another data point: Axe-Edit has lost communication with Axe_FX a few times while I was switching back/forth with Logic 9.1.7., both connected via Axe-USB. The only thing that would get them talking again was to reboot both AE and the Axe.
This particular situation was using a 2008 Mac Pro, 18GB ram, 10.6.8.