As mentioned in the main article, there is an option called "Delete empty metafields":

This option comes really handy for those of our users who prefer managing data with CSV spreadsheets. Let's see how to use it in detail. First of all, you need to prepare a CSV spreadsheet with the following columns:

1) resource identifier (product ID, collection ID, order ID, product handle, etc).

2) metafield namespace.

3) metafield key

4) metafield value (leave it empty if you want a metafield to be removed, otherwise existing metafield with the same namespace and key combination will be updated with the value from a CSV file).

This option is compatible with both file formats:

1) the "rows" 

2) the  "columns"