I had this dilema last week
Fly-Be actually send you an email after booking pointing out that Li-Ion batteries cannot be carried
I had booked 15Kg of hold luggage and this was for some spares & a change of clothes.
When I rang up to enquire about laptop & phones They said this is fine in hand luggage, so I asked if I could take a cordless drill with me. (Also Li-Ion) and they said it would have to be in the hold. I asked for an email confirming this.
So I arrived at the airport and checked in my bag, it was a tool case with the name and make of the drill & also mentions in large letters Li-Ion. The girl at checkin said sorry we are not supposed to carry them in the hold, but you can't take them as hand luggage, I showed her the email advising that I could take it and she said, 'Oh ok that must be fine then'
No issues what so ever