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.
Now, let's see how to use it in details. 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).
Here is a screenshot showing a sample file structure:
In this particular case, a metafield with namespace "shipping_info" and key "delivery_method" will be deleted for rows #3 and #5. The same metafield will be updated for rows #2, #4 and #6 with the values from the file.
Please note that bulk actions are irreversible. We encourage users to create a metafield backup using the data export feature prior to running any bulk actions.