For food manufacturers, re-process/rework is covered in TECHNICAL SPECIFICATION ISO/TS 22002-1 Prerequisite programmes on food safety — Part 1: Food manufacturing as part of the FSSC 22000 Certification Scheme:
Section 14 Rework
14.1 General requirements
Rework shall be stored, handled and used in such a way that product safety, quality, traceability and regulatory compliance are maintained.
14.2 Storage, identification and traceability
Stored rework shall be protected from exposure to microbiological, chemical or extraneous matter contamination.
Segregation requirements for rework (e.g. allergen) shall be documented and met.
Rework shall be clearly identified and/or labelled to allow traceability. Traceability records for rework shall be maintained.
The rework classification or the reason for rework designation shall be recorded (e.g. product name, production date, shift, line of origin, shelf-life).
14.3 Rework usage
Where rework is incorporated into a product as an “in-process” step, the acceptable quantity, type and conditions of rework use shall be specified. The process step and method of addition, including any necessary pre-processing stages, shall be defined.
Where rework activities involve removing a product from filled or wrapped packages, controls shall be put in place to ensure the removal and segregation of packaging materials and to avoid contamination of the product with extraneous matter.
Also Note: 10.3 Allergen management
Rework containing allergen(s) shall be used only:
a) in products which contain the same allergen(s) by design; or
b) through a process which is demonstrated to remove or destroy the allergenic material.
NOTE For general rework requirements, see Clause 14.
The requirement for rework to be covered in your flow diagram is stipulated in ISO 22000 Clause 126.96.36.199 Flow diagrams
Flow diagrams shall, as appropriate, include the following:
d) where reworking and recycling take place;
To get more specific advice you should let us know the products you are talking about and the rework operations.