Delete similar values in dictionary of 2dlists

I think you are on the right track, one easy to implement solution could be to just create a merge_years function and use that within a dict_comprehension:

def pretty_print_simple_dict(d):
    print("{")
    for key, value in d.items():
        print(f"\t{key}: {value}")
    print("}")

def merge_years(lst):
    year_counts = {}
    for year, count in lst:
        year_counts[year] = year_counts.get(year, 0) + count
    return [[year, total] for year, total in year_counts.items()]

d = {
    'Hello': [[2001, 45], [2003, 52], [2001, 6], [2002, 90]],
    'Jello': [[2009, 3], [2003, 4], [2009, 17], [2009, 1], [2009, 1],
              [2002, 11]],
    'Cello': [[2001, 5], [2001, 2], [2001, 6], [2001, 3]]
}

d = {k: merge_years(v) for k, v in d.items()}
pretty_print_simple_dict(d)

Output:

{
    Hello: [[2001, 51], [2003, 52], [2002, 90]]
    Jello: [[2009, 22], [2003, 4], [2002, 11]]
    Cello: [[2001, 16]]
}