Flown over, he had covered it (7)
I believe the answer is:
hovered
'flown' is the definition.
(hovering is a kind of flying)
'he had covered it' is the wordplay.
'he had' becomes 'he'd'.
'covered' means one lot of letters goes inside another.
'it' becomes 'over' (I can't explain this - if you can you should give a lot more credence to this answer).
'hed' enclosing 'over' is 'HOVERED'.
'over' is the link.
Can you help me to learn more?
(Other definitions for hovered that I've seen before include "Floated" , "Remained in the air without moving" , "Remained in the one place in the air" , "Hung in the air" .)