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What happened to the ball turret before a belly landing?
Short answer
In a belly landing the ball turret would likely be destroyed by the lack of clearance under the fuselage. The B-17 "Carolina Queen", unable to lower its gear, was passed tools in flight by cable and released its turret over the English Channel before landing on its belly.

Why the ball turret got in the way
If an aircraft had to make a belly landing, for example after a landing gear system failure, the ball turret would likely be destroyed by the lack of clearance under the fuselage. Whoever occupied that position was in a precarious situation if they failed to get out of it in time.
The case of the "Carolina Queen"
Unable to lower the wheels into the normal landing position, Lieutenant Bond was forced to keep circling until what is believed to have been the first successful tool-passing in the European Theatre of Operations (ETO) was completed. Lieutenant Colonel Conway S. Hall, the group's deputy commander, flew the Fortress from which the special tools to release the "Carolina Queen"'s ball turret were passed by cable to a crewman at the latter aircraft's radio hatch. With the tools delivered in this way, the turret could be loosened and eventually fell into the English Channel.
How the landing ended
Bond returned to base and brought the bomber down there in a perfect belly landing. The manoeuvre was easier for both pilot and aircraft once the turret, which protruded from the fuselage and placed it under strain, was gone. The only damage was a bent propeller and a scraped undercarriage, and the aircraft was expected to be flying again very soon.
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