Step 1 :  We Need To noupdate set to False for mail template.

<function name="write" model="ir.model.data">
    <function name="search" model="ir.model.data">
        <value eval="[('name','=','email_template_edi_invoice'),('module','=','account')]"/>
    function>
    <value eval=" {'noupdate': False} "/>
function>

Step 2 : Override The Content and Changes as per our Custom Need.

<record id="account.email_template_edi_invoice" model="mail.template">        
    <field name="body_html" type="html">
        Here Mail Template Content.
     <field>

That's it...Thank you.

You should create an migration script, under your module, in order to deactivate the noupdate in the mail.template models to be able to update them in the -u process.

First create the next dirs

- migrations/module_version/

ej: migrations/11.0.2.0.2

And inside module version dir create files, post-migration.py and pre-migration.py

where you can made your script, something like the following:

https://gist.github.com/hugho-ad/8d4fa191f2484d3eaab3f87ed4110a01