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thank you for your response 
firstly, I think this fixed my tetrapod units (A+B) and now each of them is now a single polyline instead of broken two ones.
Second, now looking at your script, I realized that entwine preserves the branches, my tree was messy because i was using āmergeā instead.
but right now, I am still trying to have control separate tetrapods (A+B units).
here is what I mean, first we have Unit A and Unit B, and we can see here that unit A is surrounded by a bounding box for clarification
then we made transformations:
we made some arrays and move transformations, and we lost control over unit A, now we only have control at the level of a larger bounding box, and then some more
array, leaving us with a a bounding box surrounding an entire layer/floor.
my ultimate goal is to make a lattice out of units A and B, which we successfully have (4 layers), but then I want to have a separate bounding box for each unit in the entire structure afterwards (like the control we had before making our arrays and transformations, but for each unit in the lattice), because i want make a multipipe for each one, the lattice is made from separate multipipe pieces, but to do that i need to have bounding box for each tetrapod (units A and B), because this lattice is supposed to be built from identical modular pieces.
maybe my earlier post can clarify what i am exactly seeking, in this thread, Riccardo helped me make the multipipe work, but I couldnāt apply his solution to a tetrapodal lattice like the one in this main thread, because I couldnt figure out how to box array a tetrapodal lattice (due to geometrical reasons).
if you could provide more help i would really appreciate it, thank you