Jennifer,
The Save to Chart button is always there. It never goes away. As long as the message is highlighted and therefore present as a message with all of the patient information in the bar next to the red paperclip, then on the right, you will always see the following from top to bottom:
Refill Meds
Pull Chart
Save to Chart
I am not sure how you are missing that. From what you wrote, it sounds as if you are looking IN the message window rather than to the right of it.