Hmmm, struggling with sore, cracked nipples sounds like a latch issue from the beginning! Or a possible tongue-tie, which was my problem. Thrush is a real concern! It usually does not go away on its own. Yeast is a stubborn beast! Blah! Definitely check with your LC about it, because if you've been struggling with cracked nipples that won't heal despite exclusive pumping, thrush could be the cause--yeast will prevent cracks from healing. If I were you, I'd start probiotics for myself and baby asap. An all-natural food store or pharmacy will have something good; I'd recommend liquid drops for baby rather than powder, which I found quite difficult to give to an infant. I put a few drops on a small baby spoon, then see if baby will take it off the spoon. You could also express a few drops of bm to mix with so baby won't spit it out. If your LC sees thrush, and especially if you see it in baby's mouth (will look kinda like cottage cheese clumps that won't come off, or if they do the skin will be red and raw), you should seek treatment asap. If you've been dealing with thrush for a long time (hence the non-healing cracks), a 14 day course of fluconazole would be what I'd try, but you'll need a script so you should find a Dr who is more knowledgeable about thrush/breastfeeding. For baby, the nystatin drops worked for my sister's LO, but I used the gentian violet which treated me and baby. Again, talk with the LC to figure out the best course of treatment and what will work for you.
I will add, that if you're dealing with yeast, you need to sterilize everything that comes into contact with baby's mouth and your breasts. Bottles/bottle nipples, breast pump parts, etc, should be boiled for 15 mins. Clothing, bras, burp cloths, etc, can be soaked in a vinegar/water solution, then washed in very hot water. Unfortunately, yeast live on all types of surfaces, so even if you're treating for it with medicine, you can become re-infected if you wear clothing or use pump parts or bottles that have not been sterilized. Boo yeast!
I only stress strict vigilance with yeast treatment because I've had previous struggles with yeasty-beasties. When I was pregnant, I had stubborn vaginal yeast that would not go away with the topical creams or home remedies. Only gentian violet worked (couldn't take diflucan while pregnant, but is ok with breastfeeding). So I've made it my goal to defeat the yeast!
Good luck with your treatments. If your mastitis doesn't feel better in a few days, check back with the Dr b/c some antibiotics won't work b/c the bacteria that causes mastitis is resistant (like Keflex). Do try to nurse if at all possible. What causes mastitis, besides non-healing cracks that provide an open door to bacteria, is milk that sits in the breasts and allows the bacteria to multiply. Nursing will empty the breast better than pumping, unless baby is having transfer issues. Also try to get the APNO or make some yourself b/c this will help in healing the cracks, along with the treatments for mastitis and thrush, if it is determined you have it as well. Wishing you the best!