I am trying to make a duplicate list of lists and change one element to another within the nested lists of the duplicate list but am having some trouble. How I made the dup
What you're doing here is a shallow copy of the list, so when you change the copy, the original changes as well. What you need is deepcopy
import copy
order = [['yhjK', 'F'], 'gap', ['bcsA', 'F'], ['bcsB', 'F'], ['bcsZ', 'F'],
'gap', ['yhjK', 'R']]
order_1 = copy.deepcopy(order)
# Now changing order_1 will not change order
order_1[1] = ['TEST LIST']
print order[1] # Prints 'gap'
print order_1[1] # Prints '['TEST LIST']