When the plugin is trying to generate the “normal” URL based on the old affiliate URL, some asumptions are made. The plugin need to remove as much of the superficial part of the URL, but not TOO much so the newly generated affiliate URL won’t work.
In some cases the plugin can not generate the correct “normal” URL. That is why the plugin contains an “edit” option so that you can adjust the normal URL manually.
Either way, even if you do not adjust the normal URL manually, the new affiliate URL should still work just fine.