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I think it'll look different in the long run.
Literal
Long-eye [with-で] look-[if-ば], come-to-differ [quotative-と] think.
Built around the idiom 長い目で見る ('to look with a long eye' = to take the long view). 違ってくる uses the auxiliary ~てくる to signal a gradual shift into a new state over time, not 'will be different' as a static fact. As usual, both the one doing the looking and the thing that will 'come to differ' are omitted — context supplies them.