I don't quite follow. Are you saying that you've made changes to your theme file that aren't reflected in the view(s)?
Anyway, check your Console (Ctrl-apostrophe or Ctrl-back-tick) for any error messages. You could also exit ST, find the themes' .tmTheme.cache file, delete it and restart ST. This will force the theme to be re-loaded (cached).
There might be an error in the theme file but this would normally cause it to fail completely (sometimes defaulting to a single colour), rather than partially.