I'm also trying to update my POD XT to V3 I tried safe mode I tried MIDI to USB cables but it doesn't let you update it offline like you said. Hopefully there's a way or maybe there can be a 3rd party solution to this.
I was having this issue. I was using an older version on the HX EDIT SOFTWARE, while the firmware on the HX STOMP was 3.11. I downloaded the newest version of HX EDIT SOFTWARE and that fixed it.