Originally Posted by bookfanmd
I have removed all the plugins as directed above and reimported all the new ones again. It did save my customizations though so I'm not sure they were removed completely.
Yes, as long as you hit "Apply" the plugins will be removed but the "Customizations" stay. So when you load a new file type plugin (upgraded from a previous version), it should inherit the proper "Customization" information (but you can double-check that manually to be sure).