Yes, or no, or maybe.
Strictly speaking it’s a command, as if “A” would make a decision as to whether or not they should get better. I think it actually carries along the ideas of “take care of yourself” and “I hope you get better”.
I do think this line needs some transition or acknowledgment of the line before. It seems like an abrupt change. Something simple like this:
B: I took something earlier. A: Well, Get better.
2- Is “stomach ” short for “stomach ache ” here?
It’s referring to some sort of stomach problem. Maybe an ache or queasiness or something.