I solved my problem.
For anyone else who has similar problems with switching from an onboard bluetooth to a second usb bluetooth dongle:
editing 'recalbox/etc/udev/rules.d/81-bt-power.rules' did the trick. I changed Kernel=="hci0" to "hci1" and after a reboot the usb dongle powers up.
I am not sure but it's maybe necessary to additionally switch /update the default agent via bluetoothctl. Afterwards controllers can be paired manually as described here.