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x <- "(pop+corn+unicorn)-bread+salt+malt"
gsub("\\+(?=[^()]*\\))", "|", x, perl=TRUE)
gsub("(?:\\G(?!^)|\\()[^()]*?\\K\\+", "|", x, perl=TRUE)

Success #stdin #stdout 0.23s 39620KB

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Standard input is empty

stdout

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[1] "(pop|corn|unicorn)-bread+salt+malt"
[1] "(pop|corn|unicorn)-bread+salt+malt"

https://ideone.com/aZkOfB

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R (R 3.5.2)

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