TOCs don't disappear form the final document, but in the redline, it will look like the TOC has been removed and re-inserted.
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This is because the TOC is a Field in Word and all Fields are automatically updated by O&D to ensure they reflect the latest data after any changes to the document. It's like selecting the entire contents of the document in Word, right-clicking, and choosing 'Update Field' from the menu

You can check the TOC is still there in the final document / in the clean view without tracked changes.