Well this is a bag of worms
Are you Fensa registered?
Or have you got Building Control involved? They would specify/give advice.
Otherwise if your building is old and listed you will still need BCO approval but also planning and conservation departments will need to be informed to give you their approval.
For what it is worth the projecting flashing will probably be a drip strip and if it has worked for all these years I would put it back.
Other than that you don't often find flashings round windows, but timber-frame houses can be prone to leak and people nail all sorts on in an attempt to keep the weather out.