2
If you are using a cloned template set, just go to the template manager, open the cloned newbb templates, delete the templates. Then you will have an option to regenerate them.
I had a similar problem with the AMS module, but for different reasons. I had duplicate, and triplicat templates due to a bug in the early release of XOOPS 2.0.9. I had to delete and regenerate those templates. But my default templates are duplicate due to the bug.
Anyway HTH.
PS. any problems you can always revert back to the default template set.