This can be a life threatening event, especially if it doesn't evacuate and causes pressure or necrosis. This is very stressful to the puffer and can cause many problems (altered immune response, hemorrhage, bowel obstruction, etc)
I would recommend not stressing the puffer any by squeezing, or trying to get it to reinflate.
I would place the puffer in a large critter box (available at most pet shops) - make sure you get one that is vented or has vented lid. Weight the box with the puffer on the bottom. You can use live rock, tank decorations, whatever. I have had good success with this and only on rare occassions have had to use anesthesia and manually remove the air with a hypodermic needle.
Best of luck,
Kelly