I have no experience pruning lychee - this is the first year I will prune mine, after I harvest my first few fruit. So I am looking forward to watching this discussion on how lychee responds to pruning. I have a lot of other trees, and I think you are right that these scaffolds might not be optimally placed. I think if it were me, I'd take off that topmost branch and leave a stub about 4 inches above the other two branches to see if you could induce some better scaffolds to sprout (don't known how likely that is), but it would be in the position of apical dominance, so seems like that would give the best chance. And if I were doing that anyhow, I think I'd use the summer to turn that topmost branch into an air layer. It looks like when separated it might make a nice shaped tree. My lychee has a badly placed branch that I'm going to try making into an air layer so long as the branch needs to come off anyhow.
I talked to an elderly gentleman at the Orlando tropical fruit club once about how he protects his lychee from cold. He has huge trees, and he said he aims to protect 8 feet of trunk, and if he can save that much it will form a nice tree again. So lychee must be capable of resprouting from the trunk.
Can't wait to hear from the lychee experts out there! What is the ideal branch to trunk angle for a good lychee scaffold?