I have had a somewhat similar problem with R4.0.4. Perhaps it’s related?
My issue was that the USB disk device was somehow partially dismounting and then the backup process just hung while waiting for a write to complete. There does not appear to be any kind of deadman’s switch/timer while writing so it just hangs indefinitely. If I fully dismount the drive and then remount it then the backup has continued when the destination became writable again.
This only seems to happen if I am using the seprate controller assigned to sys-usb and it doesn’t matter which physical drive is attached. But if I use a built in dom0 controller and pass the same USB device to the sys-usb everything works just fine. For now that is my workaround for all long running (>90min) backups.
I have had a really hard time finding a working 4x multiport USB controller. One older chipset (don’t have that info available right now) only works in dom0 (fedora-25) and not fedora-3x as the kernel support for it seems to have been removed. The 2x USB board I now have mostly works except for this bizarre backup issue. It used to work just fine with no issues so I’m not sure what/when that exactly changed. A forced system failure/upgrade along the way also complicates the determination of the root cause.