FWIW I've not had any timeouts using the AFX II Mark I and v9 beta with AxeEdit current version. I've got several hours in with that combination, tweaking existing presets, resetting blocks, adding new blocks, creating fresh new ones, etc. I also didn't have any issues with v8.02 but didn't use AxeEdit/v8.02/AFX II rack a lot as I've been using the AX8 mainly for a few months. Just adding this info as a data point.
Windows 10, USB connected right to the PC (no hub, etc.), USB drivers were loaded to this PC August 2016 when it was brand new and never uninstalled/reinstalled. I've bounced between AxeEdit, FractalBot, and Cab-Lab 3 (uploading IR's), USB audio running thru the II rack, without any problems in a single session (a couple of hours long). I also never had any other audio programs/DAW software running during my sessions.