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iPad Air 2 Smart Covers Not Recommended for 9.7-inch iPad Pro
With the launch of the 9.7-inch iPad Pro, Apple also released a line of Smart Covers specific to the new device, which are being sold alongside Smart Covers for the iPad Air and the iPad Air 2. Given that many people may already own an iPad Air Smart Cover, there was some question as to whether it would fit on the 9.7-inch iPad Pro.
Because of the Smart Connector on the 9.7-inch iPad Pro, the magnet alignment in the Smart Cover is different, something an Apple representative confirmed to Macworld. For that reason, using the iPad Air Smart Cover with the 9.7-inch iPad Pro is "not recommended."
As for the Smart Case designed for the iPad Air 2, while it may fit, it isn't designed for the Smart Connector, the rear flash, or the four speakers on the 9.7-inch iPad Pro, making it technically incompatible.
With Apple's own iPad Air accessories ill-suited for the new iPad Pro, it stands to reason other third-party cases and covers designed for the iPad Air and iPad Air 2 are also not going to work with the 9.7-inch tablet, requiring adopters to purchase new accessories.