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At the end of most test chamber, the robots are disassembled in order to be transported to a new chamber through the pneumatic pulls of the Pipe Network. After the components of ATLAS and P-body arrive at a destination set by GLaDOS, they are then reassembled.
Occasionally, when one or both of the robots are destroyed during testing, GLaDOS comments on how the Reassembly Machine has better things to do then to constantly reassemble the duo.
Despite the community believing the Reassembly Machine and the "disassembly" machine are two different things, they are not. The arms inside the Reassembly Machine can be tasked to either disassemble or reassemble ATLAS and P-body. This is proven when the Reassembly Machine was seen in the intro video of Calibration Course and later the same machine was repurposed to disassemble the two, ultimately proving that the Reassembly Machine would be building the bots off-screen (seconds before they are spawned).
It is possible that the Reassembly Machine can be used to make other testing elements, as it was never observed exactly how a Weighted Storage Cube was built.
GlaDOS' dialogue frequently hints that the Reassembly Machines have a central AI.