I eventually sorted the problem.
Track changes were activated, but even if I was displaying the Final version (with no comments), the search and repalce function was dealing with the combination of the original and final strings together.
If anyone faced the same issue, you simply have to deactivate the Track changes.
If you activate track changes and display deletion inline with insertions, this is what you get:
Before replace: Section 2
After replace: [Section ]2[2]Chapter [brackets are for the deleted text]
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