I have Mac OS X El Capitan and Ubuntu 16.04 installed on my iMac 27" (Late 2012). There is no problem connecting my bluetooth keyboard and trackpad in Ubuntu. I can reboot in ubuntu over and over again. Still works fine on bootup! However, if I then boot in to OS X I have to pair them there again, and if I then restart in Ubuntu they have to be reconnected again. (I do this with a usb optical mouse.) Very disturbing. Help?
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This is generally how BT pairing works, your Ubuntu and OSX installs are different devices and the HIDs will need to be manually re-paired when you change os. Otherwise, other devices near by will constantly be hijacking your HIDs. – jowan sebastian Sep 15 '16 at 06:50
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most BT mouse and keyboard can only be paired to one computer (one OS to be specific) I had the same with Win/Ubuntu and MS Sculpt mouse
You can try to use the same key see here How can I avoid having to pair my bluetooth mouse all the time?
