AVR (at90usb1286) sleep and USB
IIRC electrically you just have to toggle the pull-up resistor connected to D+ (or was it D-) so I would try manually setting and clearing (with a small delay in between) the DETACH bit in the UDCON register.

In both the LUFA and V-USB libraries there were no problems with disconnecting and reconnecting to USB from software. I guess USB_Init did this by itself in those.