If that was only the main motor unit that stinks, I'd say - take a HEPA filter cartridge out and see if it stinks even without the filter. If it does not – just get a new filter.

It takes much more for the nozzle to get that smell so replacing HEPA filter only is not likely to help. Since the nozzle and the vacuum were used under the same conditions they have to be cleaned inside out. That requires taking everything apart and washing all parts. This job requires a person with a bit more advanced technical skills (not a total vacuum geek though). If you are attempting it yourself – use a digital camera; snap plenty of pictures while taking apart so you would know how it comes back together. Do only a nozzle or a unit from start to finish. You want to change BOTH filters HEPA and the motor cooling filter as they both will have absorbed that smell.

DO NOT use any fragrances or perfume as it simply will mix with the existing smell and may produce even worse stench where you will not want to even store the vacuum indoors.

Only other TEMPORARY solution that I can think of is if you use one of those KILL ODOR solutions with enzymes (no scent added). Spray in the empty water and set the Rainbow on it, spray a bit inside of the hose and on the bottom of the nozzle. Put everything in a plastic bag and leave it overnight for enzymes to work. There are all kinds of sprays out there so some of them may discolor plastic as and some may be flammable so do not spray on the top of the nozzle or the vacuum and do not turn it on right out of the bag. If it helps it will not be for very long.