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As the parent company, I would want any individual work done to benefit the main site and as a store owner, I would want to have some benefit from the parent company as well. There need to be policies in place to prevent bad practices, but it should be all stores and the parent company helping each other. If they want to be treated as a separate entity then they should probably build a website themselves on a separate domain. Most major retailers have the stores in subfolders. Go check walmart.com as an example.