Mission Control said there was no risk of it hitting the space station.
Both spacewalkers then worked to install four protective shields over Tranquility's outboard port where PMA-3 had been attached.
The duo were also tasked with installing four thermal protection shields to cover the spot on the Tranquility module where the PMA-3 was removed, but one of the shields was "inadvertently lost" during the spacewalk, NASA said. A piece of important cloth shielding to guard against micrometeoroids floated away while the astronauts were at work.
Whitson, 57, is making her eighth career spacewalk, surpassing the record of seven previously held by American Suni Williams.
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It was Whitson's eighth spacewalk, also a record for a female astronaut. There was frustration in her voice as she informed Mission Control. All equipment and tools are supposed to be tethered to the ship or to an astronaut. It's unclear what happened or who was responsible for the lost fabric shield.
The entire space station is protected, in some fashion, against possible debris strikes.
The spacewalk began at 7:29 AM (local time) when both Whitson and Shane Kimbrough switched their spacesuits to battery power. Flight controllers in Houston moved it to a new location Sunday. Mission Control instructed the astronauts to retrieve the cloth cover just removed from the docking port, and try to fashion it over the gaping hole left by the lost shield.
This will serve as the second of two docking ports for the future SpaceX and Boeing crew capsules. Expedition 50 Commander Shane Kimbrough of NASA and Flight Engineer Thomas Pesquet of European Space Agency (ESA) were the spacewalkers for first spacewalk. Whitson and Kimbrough had cameras strapped to their helmets to document their work on the livestream as the space station drifted over South Africa, then India.
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Today's spacewalk was the second in a series of three spacewalks to upgrade the exterior of the ISS with parking spots for a new generation of space taxis ferrying astronauts to the station.
She is scheduled to return to Earth in June but could stay deployed until September. A decision is expected soon.
NASA, meanwhile, has indefinitely delayed a spacewalk that had been scheduled for next week. Shipper Orbital ATK is relying on the United Launch Alliance's Atlas V to haul up the goods.
She completed the walk with her partner, current Space Station commander Shane Kimbrough, as they were preparing a docking station at the International Space Station where they reside.
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When Wilson makes her next spacewalk, likely sometime in April depending on the arrival of needed supplies, she will become the third-most-experienced spacewalker, male or female.