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^ This! Great stuff Linda, as always!

Has the main site been online for as long as the affiliates? Are you driving traffic to the main site in similar channels and volumes to what the affiliates are driving to their sites? If the content and on-page optimization is roughly the same, and if the sites have been up for the same amount of time, it's likely off-page optimization that's making the difference. The affiliates may be doing paid advertising, mentioning their sites on social media, and otherwise building a lot of links to their content that you're not doing on the main site. I would give it time and try to search for longer-tail keywords - more specific ones, so if you sell widgets, try to optimize some pages for "red curly widgets" and "blue titanium widgets" rather than competing for the more basic "widget" type keywords. The more specific you can be, while still choosing language that your visitors are searching for, the more you will see traffic rise to the main site and the better they will convert because they're looking for exactly what you're offering.