You can call embedHTML as many times as needed. But you need to add the styles to be applied each time you call embedHTML. You can't call embedHTML to add some styles, and then call again embedHTML using the styles added from the previous call, you need to add the styles again to the HTML to be added. Or you can reuse styles using custom Word styles.
We have done some quick tests using ten tables with their own styles (calling embedHTML one time and calling embedHTML for each table) and everything is working correctly. As the trial package doesn't include support for custom code, we recommend you to check the available documentation and the included samples: https://www.phpdocx.com/documentation/introduction/html-to-word-PHP
If you purchase a license do not hesitate to contact us again and we'll be able to help you with your issue.