Actually in the new PDF Reader we implemented saving of annotations and scribbles after turning to the next page (and also by closing of document) page. Does it not work for you? Did you update your device?
Battery icon will be refreshed by updating of a page only.
If you have deactivated automatic suspend mode, and let an opened document over night, next morning battery indicator could still show you 2 bars, even if the battery is almost empty and is short before allarming you with the "low battery" message. Only turning to the next page (or other action, which updates the screen) will display the correct state of the battery.