Smile and affiliate commissions are separate. So in your example both the charity and the stale affiliate link would receive a cut that is independent of the other. Source: I run an affiliate site and my links always direct to Smile, and I keep getting commissions.
Is it possible that by linking to smile, your amount is reduced by the smile amount, or that it operates differently when the affiliate link happens first and the smile insertion happens second?
I've been donating to charities through affiliate links and Smile for a while. Whenever I plan to make a purchase I go to the smile.amazon.com URL while also appending a charity's affiliate link (e.g. "/?tag=AFFILIATE-ID") to the URL.
I think charities will still get a significant amount from my purchases, since AmazonSmile was only 0.5%, while affiliate links for many categories are 4% or higher.
I always assumed Smile was mostly a way for Amazon to get me to direct that to a charity instead of a stale affiliate link.