im know expert but id trim them back to a healthy bud or branch next month before the plants come out of doremancy . perhaps the tree needs a bigger pot/planting in the ground .

unless the black is creeping along then id do it strate away .

A photograph of the tree would be good, with a close up of the problem.
Did you notice anything else? Such as curling leaves, blackened leaves, early leaf fall? Any lumps, bumps or cracks on the stems? Any raised reddish bumps anywhere, or orangey oozing, or any oozing at all?

I'm putting this comment on, because we have managed to lose three apricot trees now, and I will be interested to follow the thread.......

Did you water it every week for the first 2 years ?

Hello, all I have learned is that stoned fruit, including cherry, plum, apricot etc, should only be pruned after fruiting. As long as you don't cut into any green live wood, cut only the dead off at this time. Apricots, peaches, and similar, suffer with die-back in the summer only when the trees are insufficiently watered in dry weather and/or desperately need feeding. Mostly the latter, if you are growing in poor soil, or unfed soil ... a good dose of top rose will help. Apply now and when in fruit.