It seems to me you are confused on how languages works now in Moodle
First for the certificate module itself, there is nothing to do, if you have several languages available in your Moodle site, you have nothing to change, and nothing to upload, just go to "Site administration" -> "Language" -> "Language packs" and update the French language pack, all French strings for the certificate module will be updated.
Then, if one of your users has selected French language (or if the French course force language to French for all participants) he will see the page for the certificate module in French, and he will get his certificate in French.
But maybe you want to go further and have a special template for your French certificate ? then you need to create a new subfolder in mod/certificate/type (for instance mod/certificate/type/french/) and put a customized certificate.php into this subfolder.
See docs at http://docs.moodle.org/25/en/Certificate_customizing to learn how to customize a certificate.
Creating this new certificate template will have no effect on certificates in other English courses.
Of course when you will create your certificate in the French course, you will select this new template.