Use correct and unique EUIDs
When serving ads in email, it is crucial that your EUID macro is correct and generates unique IDs for each of your recipients. A lot of problems originate from this oversight. For more information, read Email Ads and the EUID.
Add your ad zones back
If you use Indie Email as your email platform, go to your Saved Modules and drag the email ad zones back into your template. If the issue is that your ad zones got deleted, once you drag the saved modules back in, the ads will appear.
Wrong ad type
Another possibility for an ad to not display in an email is for the wrong ad type to be assigned to the email zone.