I've been using inspect(fit, "case.idx") to see which cases have factor scores in the factor score matrix that lavaan produces, but I don't really know where to take it from there.
data("HolzingerSwineford1939")
HolzingerSwineford1939$x1[1] <- NA
example(cfa)
factor.scores <- predict(fit)
nrow(HolzingerSwineford1939) # 301
nrow(factor.scores) # 300
for (vv in colnames(factor.scores)) HolzingerSwineford1939[inspect(fit, "case.idx"), vv] <- factor.scores[ , vv]