They were still in a position of great peril, since they could not expect to embark and cross the stream without suffering tremendous loss from the enemy before whom they would be flying.
https://www.gutenberg.org/files/16167/16167-h/16167-h.htm
g. "if they tried to cross the stream then they would be flying"). From glancing at some of the surrounding context, I think perhaps the latter is the more likely interpretation.
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Looking at this sentence alone, "would be flying" is somewhat indeterminate between future-in-the-past (a kind of "past tense" of "will be flying") and result of implied condition (e.g. "if they tried to cross the stream then they would be flying"). From glancing at some of the surrounding context, I think perhaps the latter is the more likely interpretation.