Exporting/importing is not as easy as that yet as there are things that are not exported by the system. For example, the images of categories are not exported.
You should export and just import a CSV with two columns:
product_tax_id and product_code
That way, the system will just update the tax_id and not touch everything else which is already working.
That line 254 of that file should be:
$all_products[$category->product_id]->categories_ordering[]=$category->ordering;
instead of:
$all_products[$category->product_id]->categories_ordering[]=$category->category_ordering;
We'll change that on our end.