So, I'm going to stick with describing how one could do this with EP4 at the moment. Another method that comes to mind would be to "simply" export the various attributes related tables and make changes to them to match up with what is available in store 2 and then import the new/revised data. Not what I would consider a quick task.
Regarding EP4. If store 1 has a unique model # for each product and the option names are unique (only one instance of the option name in all of the option names), then the import of the first two files has populated store 2 with all of the attributes of the product from store 1. What is missing though is the detail associated with each attribute. So, to update store 2's attribute details, a file has to be generated such that each of the four primary keys match an existing entry in the attributes table. So, how to accomplish this?
Here's what I see. It is possible at this point to export the detailed attributes from both store 1 (already have) and store 2. Each of these has text versions of the option names and option values names. The model number is whatever it is and the products_attributes_id is expected to be unique to each store.
So what I would do would be to sort the data in both detailed lists on three fields in the same "order" (either ascending or descending but make it the same on both spreadsheets) such that sorted by products_model, then option_name, and then option_value_name.
Then pick the method/location desired, but the goal is to eliminate from the list for store 2 any product that is not in store 1. This would be by a comparison of products_model. For now, also eliminate from store 1 any row that doesn't have a model #. (will have to address that separately because really that product never got uploaded to store 2, but at least the list should be small.)
Then begin moving entire rows as necessary such that the row in store 1 lines up with the row of store 2 by first comparing option names then option value names. Provided nothing "new" has been done with store 2, these should line up exactly.
Then once all have been lined up, copy the primary field data from store 2 over the data of the same field for store 1. Once all four columns are copied, save the file as the csv file to be uploaded and then imported into store 2.
Obviously through this process you'll want to save a backup of the file(s) to minimize any rework. Keep in mind the filenaming convention needed by the plugin.
And with that, the new file when uploaded and imported to store 2 should have store 2 with the same attributes and details of attributes as store 1.



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