There isn’t an entry on the “Handles & Brakes” tab for the flap handle. But I was able to use FSUIPC’s monitoring facilities to observe the flap handle index behaviour. In a replay with the default Cessna 172 I see the index changing correctly as the flaps are lowered but in a replay with the Arrow, there is a fight going on. Every time the handle index is changed by Sky Dolly it is immediately changed back to zero.
I think what is happening and it may be the issue with your sliding canopy too, is that Just Flight have created an Lvar for the flap handle position in their aircraft called “LOWER_flap_handle” which is over riding the sims default flap handle index and reseting it to whatever value LOWER_flap_handle contains.