One option as a protective method is to set your template to Read Only, however this is not ideal for those utilising custom templates on a network.
A simple workaround is to set the default template located on you local drive (the default template). However in the project the template would continue to be set as the shared templates folder.
This set up should prevent your custom templates form being mistakenly over written.
C:\Users\Public\Documents\Autodesk\Inventor 2014\TemplatesOr follow the folder options on the right hand side of the image above.
Step Two is to make sure your Project templates folder is directed at the custom templates located on your network drive. The project setting overrides the setting in the application options.
Also if you find other times that your templates are overwritten this will often come about by changing the default template settings in the application options or in the start up screen. If you already have your templates created and set correctly then there is no need to change this option.