Same question here 
As far as I know, it is only possible to replace files that are within templates/www. Therefore: How did you do it? I would expect, that you have to replace the method that actually calls the navbar.html?
erpnext (or frappe)
|- erpnext (or frappe)
|-- templates
|-- www
(documented by @rahy before 
How to customisation website footer in version-12 - #5 by rahy )