Yes, "were" is the better choice.
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Ducks1160Her eyes were wide open all the time as though she were/was in a perpetual state of surprise, and they had a sad, frightened quality even when she smiled.First, don't trust a computer's judgment on grammar. Second, I don't see anything wrong with either choice. Third, the reason for using the subjunctive is not
Ducks1160Her eyes were wide open all the time as though she were/was in a perpetual state of surprise, and they had a sad, frightened quality even when she smiled.Note also:
"As if" and "as though" were originally always used to introduce
counterfactuals, but are now often used in "looks as if",