我猜关键字"timeclock_id": "528"是一个错字，应该是"clock_id": "528"。
试试看：

import json

with open("your_data.json", "r") as f_in:
    data = json.load(f_in)

df1 = pd.DataFrame(data)
df2 = pd.DataFrame(
    [
        {"emp_number": d["emp_number"], **dd}
        for d in data
        for dd in d["organization_trackings"]
    ]
)

df1.pop("organization_trackings")

print(df1)
print()
print(df2)

# df1.to_csv('df1.csv', index=False)
# df2.to_csv('df2.csv', index=False)

图纸：

id emp_number clock_id
0     181        527      124
1  181837        649      528

  emp_number                 title value value_description
0        527              Division   200              Cons
1        527              Location   951              Jasp
2        527               Special    20            Remote
3        527    Primary Department   200              DPT1
4        527  Secondary Department  2000                DH
5        527              Function  0000          Resource
6        649              Division   200        Consultant
7        649              Location   001           Atlanta
8        649              Function  0000          Resource

这检查clock_id，并且如果失败则检查timeclock_id。
工作样品：https://onlinegdb.com/WaR32RLl2

from io import StringIO
import csv, json

json_file = """\
[ { "id": 181, "emp_number": "527", "clock_id": "124", "organization_trackings": [ { "title": "Division", "value": "200", "value_description": "Cons" }, { "title": "Location", "value": "951", "value_description": "Jasp" }, { "title": "Special", "value": "20", "value_description": "Remote" }, { "title": "Primary Department", "value": "200", "value_description": "DPT1" }, { "title": "Secondary Department", "value": "2000", "value_description": "DH" }, { "title": "Function", "value": "0000", "value_description": "Resource" } ] }, { "id": 181837, "emp_number": "649", "timeclock_id": "528", "organization_trackings": [ { "title": "Division", "value": "200", "value_description": "Consultant" }, { "title": "Location", "value": "001", "value_description": "Atlanta" }, { "title": "Function", "value": "0000", "value_description": "Resource" } ] } ]
"""

with (
    StringIO(json_file) as file,  # replace with open(FILE_PATH, 'r')
    open('csv_file1.csv', 'w', newline='') as f1,
    open('csv_file2.csv', 'w', newline='') as f2):
    data = json.load(file)
    w1, w2 = csv.writer(f1), csv.writer(f2)
    w1.writerow(['id', 'emp_number', 'clock_id'])
    w2.writerow(['emp_number', 'title', 'value', 'value_description'])
    for i in data:
        _id, emp_number, clock_id = i.get('id'), i.get('emp_number'), i.get('clock_id', i.get('timeclock_id'))
        orgs = [[emp_number] + list(j.values()) for j in i['organization_trackings']]
        w1.writerow([_id, emp_number, clock_id])
        w2.writerows(orgs)