I recently made a small change to DetectSyntax that alleviates the need to have all of the default rules in a custom settings file. In the past, the settings that ships with DetectSyntax had a key labeled "syntaxes" and if you had a custom settings file in Packages/User/DetectSyntax.sublime-settings, the "syntaxes" key there would replace the default one. I changed the default key to "default_syntaxes" to avoid this problem, which means you can now just have the new syntaxes in your custom file. Small change, I know, but a long time in coming.
Everything should just work, but if you experience any problems, please create an issue and include the contents of your custom settings file and what platform you are on.