Create one controlled working version
Choose a naming convention and a person responsible for incorporating agreed changes. Preserve earlier milestone versions. Avoid several files all labelled “final” without a date or purpose.
Use a decision and comment log
Record each question, its owner, the proposed action and the decision. Distinguish language edits from scientific changes that require the responsible author. When comments conflict, resolve the issue explicitly rather than silently choosing the last version received.
Set review milestones
Schedule checks for the analysis, full draft, submission files and final approval. Specify the response date and what each coauthor needs to review. Keep enough time for affiliations, declarations and contributions to be confirmed.
Protect the submission record
Archive the exact submitted files and acknowledgement. Later reviewer responses should refer to that version. Agree any external assistance and the required disclosure, and use an appropriate channel for confidential data and unpublished material.