If you aren't trying to eradicate rust and purging foliage as well, I wouldn't be as concerned with the soil. In good conditions, more than half the daylily rust spores in one study survived just over a month in vials in the lab, they were not re-tested after that length of time so some could have survived longer:
http://web.ncf.ca/ah748/latent...
Survival would likely be different in the field. That's the only study that I know of that looked specifically at spore longevity and specifically at daylily rust. I did find some research for another Puccinia rust that showed spore viability was around a week at the most if they were covered by a relatively thin (5 mms I think it was) layer of soil, longer if they were not covered. That suggests to me that you could use your soil to partially fill the pots and then top off with a layer of new mix if you were still concerned.
Regarding resistance ratings, there is always going to be some doubt because of different environmental conditions even within a garden plus the different races of daylily rust to which a cultivar may vary in susceptibility. A single rating of resistant is always going to be questionable.
