Having similar issues with homeassistant & raspberry pi 3+. Either HW or hcitool.
Logs show escalation of issues, rebooting every night makes things work almost all the time except some occasions when things just stop working after random time since reboot.
raspberrypi kernel: [110134.572778] Bluetooth: hci0: Frame reassembly failed
raspberrypi kernel: [110885.311899] Bluetooth: hci0: command 0x1003 tx timeout
raspberrypi hass[487]: Can’t init device hci0: Connection timed out (110)
raspberrypi hass[487]: Could not open device: No such device
raspberrypi hass[487]: 2019-10-20 13:20:20 WARNING (MainThread) [homeassistant.components.sensor] Updating ruuvi_hass sensor took longer than the scheduled update interval 0:00:30