If you are using any third-party plugin to create custom data fields, then it will be stored as metadata. You may please export the CSV with the option of Hidden meta checked in the export mapping. This action will include the custom metadata fields in the exported CSV.
With custom fields created using third-party plugins, it is important for the import file to have data in the same format as required by those plugins. The easiest way to identify the format is by exporting the sample existing data/product in the site using the plugin. Make sure you have enabled the option of Hidden metadata on the export mapping screen. Use the exported file as a template to import the data back.
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