Does the civil industry use the CAN FD bus?
It's hard to prove a negative, but I would say the answer is no for the following reasons:

In all my years in the avionics industry, I've never heard of anyone
even discussing the possibility (though I realize CAN FD is fairly
recent).
There are numerous manufacturers that use ARINC 825 which is an
adaptation of the basic CAN.
The AEEC has no
active committee working to update ARINC 825 to include support for
CAN FD which would be the normal process before it would be used in
avionics.

Avionics suppliers just can't decide to use a new databus.  Their equipment has to talk to equipment from other manufacturers and if you don't have a defined protocol and agreement between suppliers it just won't work.