I just did it.
For the first 7 weeks of my DD's yeast rash, I had her in 7th generation sposies. It didn't seem to make a difference as she continued to have the rash. I just didn't want her in the sposies anymore, so I decided to try to get her back in cloth. The first couple of weeks I used prefolds at home so I could bleach them and sent her in sposies to DC. Once I ran out of sposies, I just started to send her in FB pockets. I did not bleach these, but use Grapefruit Seed Extract instead (60 drops in the hot wash). I also loaded her up with CJ's BUTTer for yeast at every diaper change. To wash her diaper area I use distilled water mixed with GSE and TTO. Her yeast is gone. I am continuing to use the GSE in her diapers now to prevent any yeast from coming back. I'm horribly paranoid about yeast since it has taken since November to get rid of it (so paranoid in fact that we are still using 7th gen at night, but I will likely switch out of those soon). She definitely still had a yeast issue when we switched back to cloth as I was using disposable liners when I had to apply the Nystatin. Also, I only used bleach a couple of times and mostly stuck with the GSE.
If you have any questions, let me know.
Re: You *can* leave baby in cloth and treat yeast
When I brought DS to the pedi for his yeast infection 2 weeks ago he said there was nothing wrong with leaving him in the CD. I did tell him about the yeast infecting the diapers so I did do a bunch of hot washes with a little bleach and a bunch of rinses and have added tea tree oil to his bum spray to help and it hasn't come back yet...knock on wood! I did use flushable liners while using the nystatin
I left DD in cloth while I treated a yeast infection. I used Lotrimin and just washed her diapers with some vinegar. I also use TTO in the water I use on the wipes, but that's it.
She had the rash before Christmas and it hasn't come back yet.
TTC since 11/05...ectopic pg 4/08...early m/c 6/09...BFP 10/5/09!

Nora B...June 15, 2010...8lbs, 8oz...Med-free birth!
TTC #2 since 7/11...cycle #3 of Clomid + IUI = BFP

Malcolm...September 21, 2012...8lbs, 6oz...Another med-free birth!
I took her out of cloth too because everything I read said you should. I have a top loader with no detergent dispenser, so both are placed in the washer directly with the diapers as the washer fills up.
My pedi said to take her out of the cloth, but my pedi doesn't know a thing about cloth diapering. In fact, she said the CJ's BUTTer for yeast would "feed the yeast". It didn't. In fact, it worked better than the Nystatin.
Pinstripes and Polka Dots has one. However, pretty much all of the sites say to take baby out of cloth while treating for yeast. As I said above, I don't think this is necessary. I initially added 1/4 cup of bleach to the diapers once the washer was full and washed as usual. I then dried them all on high. Using the GSE would be plenty after that (I use 60 drops as mentioned above). I dry everything on high except her pocket diapers, those I hang to dry. If your DS does need a prescription cream (ie: Nystatin), use a disposable liner between him and the diaper.
Please take your DS to the doctor to be sure it's a yeast rash before treating him and your diapers. GL! I hope it's not yeast.