Slightly different issue on my end... but a similar path forward may fix your issue.
My update straight failed and wouldn't allow my Stomp XL to connect via any USB to any of my PCs, and it was hung on load screen. My assumption is that the initial PC I used has some USB 3.0 conflicts and goofed the update connection. So I used my laptop without any other usb connections - restarted it, entered update mode on the XL, used Line 6 Updater to directly push 3.5 (not via HX Edit), and the update took. Hope that helps, good luck.
