Synonyms in the CSV file can override only the rows that are exactly the same.
In addition, it happens only when the same synonym was uploaded from the dashboard before.
Each synonym entry in the Algolia index has an objectID value that works as a unique identifier.
If you upload them through the API, you can specify your own value in the data structure (as seen in this document).
However, when uploading them through the dashboard, the dashboard does not support adding the object ID explicitly in the CSV format.
In that case, the dashboard generates an ID from the synonym content, and it only matches when the content of the synonyms are exactly the same.
Because of this behaviour, the dashboard can override the synonym entry only when the content is identical.
If you want to control the synonyms to be overridden, you can upload synonyms in a JSON format instead.
By specifying objectIDs in the JSON format, the Algolia engine can replace synonyms with the uploaded contents by checking objectIDs