I have recently installed Elementary OS, Loki on a Mac Mini (mid 2010).
I successfully configure a bluetooth keyboard and trackpad (both apple) using the 'System Settings::Bluetooth' panel. Pairing works fine.
If I logout and login, the paired keyboard and trackpad continue to work fine.
If I suspend and resume, Bluetooth has been disabled in the bluetooth panel and in wingpanel.
If I reboot, Bluetooth has been disabled in the bluetooth panel and in wingpanel. (same as suspend resume...but I fear root cause may be different).
To recover, I merely re-enable bluetooh and my devices re-pair.
The frustration is that I cannot use a bluetooh keyboard/trackpad which will not wake the computer from sleep or be unavailable after reboot.