Questions I want to ask are:
A desire to throw over reality a light that never was might give way abruptly to the desire on the part of what we might consider a novelist-scientist to record exactly and concretely the structure and texture of a flower.
1) Broadly speaking, i means 'something that never really existed'. eg There is an old war movie in which the British army tries to convince the German army that the corpse of an ordinary soldier is actually the corpse of an important officer who was carrying important army plans. The movie is called 'The man who never was'.
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My original understanding of the phrase is the same as yours, but I wasn't sure.
Broadly speaking, i means 'something that never really existed'.