update_field() is ACF function so I would guess the issue is with it. From quick look at source it calls get_field_object() and so on, so environment might not be sufficient for it to work correctly during import.
There is no “half” state for native meta data, either it exists in database or it doesn’t. You could try to stick with native WP API for meta data, but no idea what is actually required for ACF to pick it up properly.
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