This is a real pain point.
I know from experience that often waiting a day or so fixes the issue but sometimes it isn’t feasible to wait.
The issue usually occurs for me when I move a licensed site from my development server or from a staging server to a live location with a different domain. It happens almost every time without fail. The age of the domain is usually irrelevant for my sites and is more from transferring the site across locations.
The license usually shows up in the theme.co dashboard but won’t validate on the site.
If you search for “validation” you will see this is asked about constantly with people in the forums complaining their site won’t validate on a nearly weekly basis.
Not sure if you can fix this or provide instructions on a manual fix?