Well, digging it out and putting new soil in will get rid of the pupa at this time of year. You could try something less drastic. Remove all rhizomes that are left. Search for and destroy pupa. Turn over the soil, spading deeply so as to disturb the pupa that you couldn't find and then replant. Keep a close eye on the bed and remove fall debris where moths will lay their eggs. Some people burn off the iris and debris, scorching them, and that kills eggs too. In the early spring, you can treat with imidacloprid but it has to be done in March because it is a systemic and it only works on newly hatched borers.
Good luck!
Laetitia

Some of my 80 iris, about 15% look bad, but moving many earlier this year showed no signs of borers; moving at 40 degree nights doesn't bode well for overwintering.They are my oldest historics though not named, can I leave them until spring and then do I have to dig all of them and treat with bleach or will it be too late?

dmparmelee, this late in the year, most of the damage has been done. That's not to say some irises still couldn't rot, but the borers have already pupated or will soon do so. Were I you, I'd scratch around in the soil - especially around the bad-looking clumps - and remove and destry any pupae I found. I'd do a very thorough cleanup of iris foliage and debris in the bed later this fall and burn/dispose of it. (Do NOT compost it.) Next year, be extra vigilant for damage and squash them and/or treat with Merit in early spring.

Thanks, I'll do that. One extra cluster of one color was dug today, no borers. That's the way I always clean up for fear of having to dig all next summer if they get in.
I'll be very diligent. Thanks again.
Diana

Thanks Laetitia. I definitely will treat in the very early spring. These were my vintage tall pale yellow irises, and I do not want to lose them.

Susan

(lost my link here, finally reading replies!!)