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you need to add inline style on the email template Like

<p style="text-transform: lowercase;">{{htmlescape var=$customer.name}}</p>

also you can change function in this file

/app/code/core/Mage/Sales/Model/Order.php

public function queueNewOrderEmail($forceMode = false)
{
...
        
 if ($this->getCustomerIsGuest()) {
      $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_GUEST_TEMPLATE, $storeId);
          $customerName = $this->getBillingAddress()->getName();
      } else {
      $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_TEMPLATE, $storeId);
          $customerName = strtoupper($this->getCustomerName());
      }
    ....
 }

You need to overwrite this file

/app/code/core/Mage/Sales/Model/Order.php

To

/app/code/local/Mage/Sales/Model/Order.php

and change below code to queueNewOrderEmail function

public function queueNewOrderEmail($forceMode = false)
{
..
..
    if ($this->getCustomerIsGuest()) {
        $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_GUEST_TEMPLATE, $storeId);
        $customerName = strtoupper($this->getBillingAddress()->getName());
    } else {
        $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_TEMPLATE, $storeId);
        $customerName = strtoupper($this->getCustomerName());
    }
.. 
..
}

you need to add inline style on the email template Like

<p style="text-transform: lowercase;">{{htmlescape var=$customer.name}}</p>

also you can change via code please find function queueNewOrderEmail($forceMode = false) function you can change via php function strtolower and strtoupper

/app/code/core/Mage/Sales/Model/Order.php

you need to add inline style on the email template Like

<p style="text-transform: lowercase;">{{htmlescape var=$customer.name}}</p>

also you can change function in this file

/app/code/core/Mage/Sales/Model/Order.php

public function queueNewOrderEmail($forceMode = false)
{
...
        
if ($this->getCustomerIsGuest()) {
      $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_GUEST_TEMPLATE, $storeId);
          $customerName = $this->getBillingAddress()->getName();
      } else {
      $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_TEMPLATE, $storeId);
          $customerName = strtoupper($this->getCustomerName());
      }
    ....
 }

you need to add inline style on the email template Like

<p style="text-transform: lowercase;">{{htmlescape var=$customer.name}}</p>

you need to add inline style on the email template Like

<p style="text-transform: lowercase;">{{htmlescape var=$customer.name}}</p>

also you can change via code please find function queueNewOrderEmail($forceMode = false) function you can change via php function strtolower and strtoupper

/app/code/core/Mage/Sales/Model/Order.php