Thanks for the input on this datacommando. I tried the power on, no USB connection, with switch 2 + 3 held down. The Stomp comes up just as it did before with the additional message "Will reset Globals, Presets, IRs..." but does nothing after that.
I also noticed that after the FW is updated, the Updater screen still says firmware version not available. Wonder if there is some final check or handshake that is missing. I've opened a support ticket.