If you can show some pictures it would be helpful - assuming that you're still reading this several days later.
I don't worry about lichens as I reckon that they add an extra layer of defence to a tree: any disease has got to get through the lichen first. If you scrub them off, you may also damage the bark beneath which might allow diseases to enter the small wounds.
I think it's more likely that the lichens just happen to be living on a branch, and now it is dead, they are also using it as a food source as it rots. I suppose it's possible that some of what you call "lichens" might be wood-rotting fungi which have come to feed on the dead branch.
Probably the lichens are there because the branch was damp and shady - or maybe, given the wet weather, the branches are diseased with canker. Wet encourages canker and branches which don't get much sun are prone to dying-back as the branch can't gather enough sun to survive, or may die back as the plant allocates its resources to branches which can gather the most sunlight.
If you prune a tree in summer, it takes away the essential light-gathering leaves just as the plant has finished investing all its winter reserve into them, and when the leaves are then ready to absorb the best of the summer sun in warm temperatures, to build up reserves to kickstart the next growing season. As a result, a slow-growingsickly tree will lose a lot of its strength - and may even die - if pruned hard while it has leaves. Summer pruning should only be used to control plants with lots of new growth, and ideally only the new soft shoots should be cut back by most of their length.
Apples and pears can be pruned in winter, but cherries - and plums - however, are best not pruned in winter as they are more at risk of diseases entering the wounds if they are dormant when pruned. They are best pruned just as the buds begin to swell in late winter/early spring.
So: late winter/early spring pruning to tidy-up trees which haven't put on much new growth. Older wood can be cut into at this time. Branches which are more than an inch, or at most two inches, diameter, need to be thought about carefully as the wounds are often so large that they never heal - perhaps allowing canker to enter, or simply the common wood-rotting fungi - and the rots will slowly spread from the wound, into the trunk and hollow-out the tree, making it more prone to breaking in a storm.
Never give a fruit tree a "haircut" (i.e. don't give it an all-round shearing) like you would a hazel hedge. A bad pruning technique just shears the whole tree. A good pruning technique has several minutes of standing looking at what can be done, followed by strategic pruning, with as few cuts as possible; every wound is a possible entry point for disease, and shearing will not help produce good crops nor encourage the tree to grow nicely for the future.
Ideally, badly-placed branches should have been dealt with in anticipation of the later problems they would cause - and removed/headed-back while still small enough for the wounds to heal. Good pruning is about:
1. Where is the tree directing its growth now?
2. Where is its growth likely to go in future?
3. Where do I want it to be growing in future?
4. Are any branches weak, or disesed?
5. How can I achieve what I want for the future in terms of shape, and removal of diseased wood, by making as few cuts as possible now?
Unfortunately, most peoples approach to pruning is reactive - responding to a problem - rather than proactive to avoid the problem in the first place.