If a flying creature was guarding behind a wall and on the other side was a ranged creature would the ranged creature be able to target the flying creature which was guarding?
Only if it (the Ranged Creature) had the Indirect trait
Equally if they where in the same zone would the ranged creature be able to target the guarding flying creature?
With a melee attack: Yes or a Ranged
0-X attack: Yes any other ranged attack:No
Also if a guarding flying creature was targeted by Jet Stream would the +2 still apply since the creature had lost flying due to guarding?
No as this buff is for creatures with the Flying trait
If a guarding flying creature was pushed through the wall would the creature be attacked by the wall since it was no longer flying?
Yes, as long as the wall had the Passage Attacks trait, otherwise it would be the standard wall bash 3 dice attack.
Once a creature looses the Flying trait any of the qualities provided by flying are lost.