Updates made on the Department, Class and Location on the header line are also reflected on the line Items.

Scenario
Department/Class/Location on header or body level reflected on the line items of a transaction.

Solution
When preferences are set as follows on, Setup > Accounting > Accounting Preferences > General tab > Classifications section:

Allow Per-Line Department = True
Allow Per-Line Class = True
Allow Per-Line Location = True

A. Reflected on Department/Class/Location on line item.
This happens when Department/Class/Location fields are hidden on transaction form.
It is as if the preferences are turned off.

B. Not reflected on Department/Class/Location on line item.
If Department/Class/Location on line item are exposed.
Changing the header Department, Class and Location will not update the line items Department, Class and Location