Hi,
What version of OneNote do you use?
How did you create the template? Is it a page template, a section template or a notebook template? I've tried creating a notebook template and the internal links work properly when create a new notebook based on the template. Please have a look at the following article and check if you have created the template correctly. See:
If the template is created correctly, please also check the internal links. To do this, open the template, right click on a internal link and select Edit Link. Then, check the Address field to see if it's directing to the correct place.
Please let me know the result.
Regards,
Steve Fan
TechNet Community Support