301 redirect question

For SEO reasons, I'd like to change one of my sites from .php file extension to .html

I know the proper way for rankings purpose is to use a 301 redirect in htaccess file. However, I'm not 100% sure how to do this without affecting certain folders (such as blog, forum, billing software). They must be untouched and continue using their own .php files.

Can someone explain how I can work around this and provide a sample 301 line to achieve this?

Are 301 redirects bad for SEO in the long run?

Thanks