The presence (or absence) of the file(s) on the server has no direct effect on the database. Certainly opening EP4 to see no files may leave one feeling empty as well, but it will not remove or adjust any information in the database by being deleted (just like the that there is no change by uploading the file(s)).
That said, it may be worth maintaining a certain amount of history of operations/changes, but they do not have to stay on your server.
For others desiring to use EP4 to delete a product, change the status of the product to 9, then import the file/product and it and all of its linked versions will be removed from the database. To reassign a product's master_category_id which will remove it from the previously designated category, use a value of 7 as the product's status and the product's master_category_id will become that of the category for the current row.



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