lookup = ['Chicken','Burger','Ham','Salmon','Chicken Breast']
example = [['Burger','1'], ['Ham','3'], ['Salmon','0'], ['Chicken','5'], ['Chicken Breast','2']]

ctr=0
for y in lookup:
    example = [[x.replace(y,str(ctr)) for x in l] for l in example]
    ctr=ctr+1
print (example)

import re
ctr=0
for x in lookup:
    example = [[re.sub(r'b'+x+r'b', str(ctr), y) for y in l] for l in example]
    ctr=ctr+1