My guess would be transplant shock. Give them some more time to establish some new roots. Did they fruit while in the containers? I would have just got a couple of new young trees then mess with giant rootballs :)

Some trees are more resistance than others. I have had it in my orchard on a number of trees, yet other trees were not affected. At times I have had fire blight so bad I could see the bacterial ooze dripping off the blossoms. But, as mentioned no infection on other trees. If I felt like I needed to do something, my first action would be to do just what you suggested. I have thought about trying to remove the canker tissue, but never have tried it. Canker blight that overwinter can cause water sprouts to become systemically infected by the fire blight bacteria if its on a nearby overwintering canker. If I cann't remove the whole branch because the canker is on the trunk, I just leave it alone. However, I do spray the trees with Kocide (copper) along wih my dormant oil spray and maybe it helps, but I am not sure it does much for the fire blight. There is a lot of information on fire blight and all of it does not agree. Studies have been done where it has not helped even to cut out the first strikes, just leave it alone until you do your dormant pruning and then cut out the dead branches. I used to put a lot of time and energy into fire blight, but now I take a more casual approach to it. I have had a lot worst looking trees than yours and one time ordered a new tree to take the place of the fire blighted one, just to pick a couple box of apples off of it this summer. I sprayed painted all the strikes with red paint, then pruned out all the branches during my late winter purning. The tree looked like Charlie Brown's Christmas tree, but is now doing well. Go ahead and try what you suggested. Unless you completely girdle the trunk, it should not harm the tree too much. Use it as a learning experience. See what works and what does not work. I have had some trees die from fire blight, replaced them and they again died. Now, I avoid that particular variety.

Without pretending to be an expert, I can tell you the methods I use on apples, pears, and peaches. When a fungal canker occurs on a limb, I remove the limb about a foot below the canker and spray the entire area and tree with copper fungicide. This usually works. If the fungus is truly systemic, it may reappear. A trunk canker is the worst kind. You can't realistically amputate the entire tree, even though this might work in the long run. Because the fungus is contagious and can spread to other trees, I use a small spray bottle of rubbing alchohol numerous times while cutting away diseased tissue. Then, spray with copper fungicide. The following day, I coat the area with iodine and cover with a black tar, like Tree-Coat wound dressing. When dressing the wound, fill the cavity so that it is even with the surrounding bark...no cavity left. I also spray the entire tree with copper fungicide. I repeat the copper fungicide spray Spring and Fall. The success of this method requires the removal of all diseased material. This material should be burned or otherwise removed from the area. Keep a close watch on the treated tree, as well as any other trees in the area. Copper fungicide spray would be recommended for all fruit trees in the area. Certainly, someone will disagree with the above methods. I am open to better ideas.

No, don't scrape. Put on a garden glove and gently rub off the super loose stuff, maybe, but you don't want to open any more wounds. I'd just leave it, and if stuff flakes off, repaint. A commercial grower told me the following: Keep in mind that peach/nectarines are short lived trees. In commercial orchards they pull them out about every 12 years. This is because wounds (such as got from pruning) on peach/nectarine never heal that well. They heal over on the surface (sometimes) but not inside. This is unfortunately illustrated by your photos. Plums can live 25 but usually not much longer. Stone fruits in general are short lived. The most long-lived fruit tree (setting citrus aside) is the apple. This is because apple has an exceptional ability to heal its wounds.