I can't imagine any part of the upgrade would remove a template.
Do you still have a copy of the 3.11 database? If you check the table, for example with SELECT * FROM mdl_customcert_templates WHERE contextid = 1, is this template present?
If so, check the 4.1 database and see if the template is now missing.
Could it have been accidentally deleted manually? Recent versions of the plugin will add a log entry with event name Custom certificate template deleted.