A departure is something that is intended by the designer, does not comply with the Regulations, but the designer attest will offer the same degree of safety as would be achieved by compliance with the Regulations.
For example:
If changing a CU where there is no CPC on the lighting circuit, the advice given in the ESC BPG is to install a 30mA RCD, use class II fittings andplace a warning at the CU.
Such would be a departure.
Anything else would either require rectification before the Certificate was issued, or a note in the section for comments on the existing installation.