You may need to add the domain to the explicit list of allowed sites. If the domain changes within the site, that would need to be added as well (e.g. www.adobe.com and helpx.adobe.com are not considered the same).
Google also implements a Site Engagement Index score. If that score is too low, it'll block Flash, even if Flash is enabled. Go to chrome://site-engagement and look for the site in question. If the associated score is less than 100 Google will block the site. You can manually edit the score and set it to 100.
An alternative is to white-list all sites by adding https://* and http://* to the list of exceptions in chrome://settings/content/flash