Hope you are doing well.
As you are known to the fact that Let's encrypt is a third party service we provide for free to our valued customers. Therefore, there are some limitations also implied on us by them, one of them is regarding the .htaccess.
What happens in this scenario is that if any customer's is using a site that contains certain redirection in it's .htaccess the cert bot of Let's encrypt is not able to access the domain and the process of installation and re-newal is comprised. Therefore, customer's facing such issues are recommended to disable the .htaccess for a time being ( this could be done be simply renaming the .htaccess file to .htaccess.bak) , the installation / re-newal process should be proceeded once it is done and upon successful completion of the process , the .htaccess file could be renamed back to it's original form.