In microflow 1 I do not see you attaching the list to this helper object with a reference. I would also create another reference and attach a newly created object containing the fields you want to mass update. Show that object in the page you show so the end user can change the fields it wants to mass update. Create a proces button passing the helper object. Then in microflow 2 retrieve the list and retrieve the newly created object both over their seperate references. Then indeed iterate over the list and change each of the fields by checking if the value of the newly created object is not empty. When empty do not change the attribute and when filled copy the attribute value from that newly created object to the iteration. And indeed commit the list and delete the newly created object and the helper object and close the page.
For that object containing the fields you can either use the same entity or copy the entity to a non persistent object you attach to the helper object. The advantage of a non persistent shadow entity is that you do not have to clean it or delete the object afterwards. Entities with autonumber for instance would give gaps etc when you delete the object afterwards.
Hope this helps.