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Hi @Paul Heath Armengol ,
When you define your import, you will have to set up an object type mapping. While doing so, you will be offered the option what you want to do with missing objects. If you select remove there, only objects present in your csv file will persist. See this support article for a bit more details.
As a recommendation, try this in a sandbox or test environment first so you can verify what happens to your data before running this in production. Deleting data is usually quite destructive.
Hope this helps!