I recommend to be safe that you go into those templates and save any custom edits that you may have made (if you made any). Then you should be safe to merge those. If any edits are lost, you can then re apply them.
If you would like your board upgraded to the latest version of XenForo, feel free to check this thread out:http://xenforo.com/community/threads/technology-hub-xenforo-installation-upgrade-services.45948/
The style they are using can be purchased here - http://pixelexit.com/xenforo-styles/fusion-gamer-style.7/viewproduct
Yes, the style will be updated (when required) to bring it up to date with XenForo updates.