I kind of figured that Omega could be programmed through a JTAG interface (in fact I vaguely recall some article that mentioned that early Omegas demoed needed a PC to "program" the FPGAs prior to startup which I presumed at the time was via JTAG).
My original concern about the "reflashing" was *not* about the practicalities (e.g., could you use JTAG) but rather the availability of the appropriate image data in order to do it and as Ian you've confirmed they [MD] have not supplied you with the required data. The other issue is some FPGA's have a "Security" feature that prevents them from being read - if that's the case for Omega then either (a). MD have to provide the data (b). Someone who already *has* the data is prepared to share it.
It should not fall to MD's own customers to fix the computer or require the public spirited efforts of Peter Naulls - it's *MD's* responsibility. They should, IMHO, put structures in place so that they're customers are adequately supported.
The most relevant reference to USB work being done (or not) for the Omega was one I found from drobe [link] were in April 2004 Simtec denied doing any work on Omega inspite of MD apparently suggesting that they were. I don't know if that changed later - or if Stuart Tyrell was "roped into it" as it were (the clear inference from the article was that Simtec thought MD were implementing their own USB stack). Unless Stuart has committed publically to do it for them then I'd be sceptical about the likelihood of it happening.